=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo Source: iqtree Version: 2.0.7+dfsg-1 rebuilderd-worker node: osuosl42-amd64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 02 Mar 2026 10:01:03 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [137 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [137 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [96.5 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [153 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,464 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8,308 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.5 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.4 MB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,572 B] Get:22 https://deb.debian.org/debian experimental/main Sources [440 kB] Fetched 34.2 MB in 31s (1,090 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.0.7%2bdfsg-1.dsc' iqtree_2.0.7+dfsg-1.dsc 2236 SHA256:c1816ee1b75fba067a2600097a12525f94939863118d5269296254195674544e 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.0.7%2bdfsg.orig.tar.xz' iqtree_2.0.7+dfsg.orig.tar.xz 1581628 SHA256:95a3a9c3b32aeb8caa63307808fed7fad68f20f877f3fe5fe751af1d49cbdb86 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.0.7%2bdfsg-1.debian.tar.xz' iqtree_2.0.7+dfsg-1.debian.tar.xz 20020 SHA256:704055ba4585527dacedf6b6cdf5d796c4fd20828fcd48c4d6856601b422e9d6 95a3a9c3b32aeb8caa63307808fed7fad68f20f877f3fe5fe751af1d49cbdb86 iqtree_2.0.7+dfsg.orig.tar.xz 704055ba4585527dacedf6b6cdf5d796c4fd20828fcd48c4d6856601b422e9d6 iqtree_2.0.7+dfsg-1.debian.tar.xz c1816ee1b75fba067a2600097a12525f94939863118d5269296254195674544e iqtree_2.0.7+dfsg-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 02 Mar 2026 10:01:36 +0000 | +------------------------------------------------------------------------------+ + niceRebuilding iqtree=2.0.7+dfsg-1 in /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs now. /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderd5aFT8T/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/iqtree-2.0.7+dfsg I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20241127T204405Z sid InRelease [202 kB] Get:3 http://snapshot.debian.org/archive/debian/20241202T150356Z sid InRelease [202 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages [10.3 MB] Get:5 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 Packages [10.0 MB] Get:6 http://snapshot.debian.org/archive/debian/20241202T150356Z sid/main amd64 Packages [10.0 MB] Fetched 30.9 MB in 3s (12.1 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20241127T204405Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20241202T150356Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Fetched 13.0 MB in 0s (170 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp10fblp5/libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Fetched 43.3 kB in 0s (1953 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpivxq62_a/python3-defusedxml_0.7.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Fetched 54.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7tsruucx/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 sgml-base all 1.31 [15.4 kB] Fetched 15.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5wb86b4/sgml-base_1.31_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Fetched 129 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo0g9zfpf/libidn2-0_2.3.7-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Fetched 189 kB in 0s (17.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv1dwyzur/libelf1t64_0.192-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Fetched 19.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmenl6bkw/libfile-stripnondeterminism-perl_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Fetched 38.7 kB in 0s (1889 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg7mip0g8/libdrm2_2.4.123-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 grep amd64 3.11-4 [431 kB] Fetched 431 kB in 0s (36.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmputr5_m3f/grep_3.11-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dpkg amd64 1.22.11 [1531 kB] Fetched 1531 kB in 0s (92.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49fvrq8a/dpkg_1.22.11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Fetched 10.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr65jdonh/libtirpc-common_1.3.4+ds-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Fetched 73.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxkdskkx8/python3-typing-extensions_4.12.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxxhash0 amd64 0.8.2-2+b2 [26.6 kB] Fetched 26.6 kB in 0s (1025 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpocvet3o2/libxxhash0_0.8.2-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Fetched 119 kB in 0s (1626 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiq46u9sj/python3-jinja2_3.1.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Fetched 182 kB in 0s (5576 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpecc4_95f/libnl-route-3-200_3.7.0-0.3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Fetched 815 kB in 0s (28.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9l_iq6z_/libpython3.12-minimal_3.12.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Fetched 36.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbj5s6dvs/libmd0_1.1.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 time amd64 1.9-0.2 [50.8 kB] Fetched 50.8 kB in 0s (490 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8g9b1k2f/time_1.9-0.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gettext amd64 0.22.5-2 [1601 kB] Fetched 1601 kB in 0s (95.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptnrd5b0m/gettext_0.22.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Fetched 188 kB in 0s (8828 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb03ufutt/libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Fetched 37.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxfsamjyb/libbz2-1.0_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Fetched 2804 kB in 0s (30.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprc78w73j/libc6_2.40-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Fetched 2674 kB in 0s (21.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm4wwa4py/libgcc-14-dev_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Fetched 2369 kB in 0s (40.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2amawytn/libstdc++-14-dev_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtool all 2.4.7-8 [517 kB] Fetched 517 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpogg517b5/libtool_2.4.7-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libbinutils amd64 2.43.50.20241126-3 [532 kB] Fetched 532 kB in 0s (11.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaz0t2aye/libbinutils_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dpkg-dev all 1.22.11 [1332 kB] Fetched 1332 kB in 0s (83.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzkm7oci3/dpkg-dev_1.22.11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Fetched 57.3 kB in 0s (5484 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ppohgit/libsasl2-2_2.1.28+dfsg1-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpam-modules amd64 1.5.3-7+b1 [267 kB] Fetched 267 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphmvq_4ev/libpam-modules_1.5.3-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Fetched 1568 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5q0nt4d4/cpp_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Fetched 298 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphyjy3j_r/openssl-provider-legacy_3.3.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241202T150356Z sid/main amd64 openmpi-common all 5.0.6-2 [97.2 kB] Fetched 97.2 kB in 0s (4031 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1ihjxde/openmpi-common_5.0.6-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.45-3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp08pd48hs/libmagic1t64_5.45-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 init-system-helpers all 1.67 [38.7 kB] Fetched 38.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpudxp_23r/init-system-helpers_1.67_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Fetched 1966 kB in 0s (18.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt34eb38t/libpython3.12-stdlib_3.12.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Fetched 2729 kB in 0s (24.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx_ugto2a/libasan8_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcap2 amd64 1:2.66-5+b1 [27.8 kB] Fetched 27.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libcap2_1%3a2.66-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpq8o0mv2e/libcap2_2.66-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ybx1vf_/gzip_1.12-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Fetched 116 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6j7u5imq/libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Fetched 132 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpacj74gq6/libevent-core-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] Fetched 275 kB in 0s (13.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpec2uezpw/libpcre2-8-0_10.44-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnettle8t64 amd64 3.10-1+b1 [305 kB] Fetched 305 kB in 0s (30.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpare7o_z3/libnettle8t64_3.10-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 perl-base amd64 5.40.0-8 [1675 kB] Fetched 1675 kB in 0s (97.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptj_8offq/perl-base_5.40.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcap-ng0 amd64 0.8.5-3+b1 [17.5 kB] Fetched 17.5 kB in 0s (820 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttcbqin1/libcap-ng0_0.8.5-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Fetched 181 kB in 0s (17.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5i769ctm/libpsm2-2_11.2.185-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Fetched 9092 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnegztv0i/libkeyutils1_1.6.3-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Fetched 8877 kB in 0s (43.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8qz5guh/libamdhip64-5_5.7.1-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Fetched 128 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw38rny7j/docutils-common_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Fetched 7984 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwm17ok4c/python3-jaraco.context_6.0.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Fetched 164 kB in 0s (2121 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4wu00gql/libhwloc15_2.11.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Fetched 27.8 kB in 0s (960 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lctihbq/python3_3.12.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libctf-nobfd0 amd64 2.43.50.20241126-3 [155 kB] Fetched 155 kB in 0s (5346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8f4g8_z/libctf-nobfd0_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Fetched 213 kB in 0s (8288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn9ukg8bo/python3-pkg-resources_75.2.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Fetched 42.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0wfw8_6j/libpipeline1_1.5.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libzstd1 amd64 1.5.6+dfsg-1+b1 [300 kB] Fetched 300 kB in 0s (8512 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnvq2blvc/libzstd1_1.5.6+dfsg-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Fetched 59.4 kB in 0s (2531 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf5t7uca6/libnl-3-200_3.7.0-0.3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Fetched 200 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiynvvnz2/libnl-route-3-dev_3.7.0-0.3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB] Fetched 704 kB in 0s (54.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp96rran92/libdb5.3t64_5.3.28+dfsg2-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcrypt1 amd64 1:4.4.36-5 [89.8 kB] Fetched 89.8 kB in 0s (8861 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.36-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpwmkzyj4i/libcrypt1_4.4.36-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Fetched 324 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_907kb3e/libkrb5-3_1.21.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gcc-14 amd64 14.2.0-8 [530 kB] Fetched 530 kB in 0s (30.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6_utjfss/gcc-14_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Fetched 170 kB in 0s (1843 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphgx506si/libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqxnxrojm/help2man_1.49.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Fetched 14.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9rzn06jr/pkg-config_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Fetched 913 kB in 0s (69.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj1pkwuds/libsqlite3-0_3.46.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplr_kaytf/xml-core_0.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 autopoint all 0.22.5-2 [723 kB] Fetched 723 kB in 0s (56.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbf4stkbc/autopoint_0.22.5-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (55.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy0yr9847/findutils_4.10.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Fetched 22.3 kB in 0s (766 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt5od3344/libdrm-amdgpu1_2.4.123-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Fetched 132 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpriz3dbla/librhash1_1.4.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB] Fetched 91.2 kB in 0s (2227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkcstybkk/libsemanage2_3.7-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 adduser all 3.137 [140 kB] Fetched 140 kB in 0s (2161 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm6ucjvp1/adduser_3.137_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Fetched 305 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptcjn07v7/libevent-dev_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 base-files amd64 13.6 [72.8 kB] Fetched 72.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxlwwnrx7/base-files_13.6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Fetched 51.9 kB in 0s (2039 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl68j77is/libpciaccess0_0.17-3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 sphinx-common all 7.4.7-4 [731 kB] Fetched 731 kB in 0s (53.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzg6bdsjd/sphinx-common_7.4.7-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241202T150356Z sid/main amd64 libopenmpi40 amd64 5.0.6-2 [2366 kB] Fetched 2366 kB in 0s (46.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmo9ns1ez/libopenmpi40_5.0.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcc1-0 amd64 14.2.0-8 [42.8 kB] Fetched 42.8 kB in 0s (1946 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxrwpvzlf/libcc1-0_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 linux-libc-dev all 6.11.10-1 [2461 kB] Fetched 2461 kB in 0s (62.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfdelad8v/linux-libc-dev_6.11.10-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Fetched 326 kB in 0s (28.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0b79zgs4/libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Fetched 23.6 MB in 0s (66.6 MB/s) dpkg-name: info: moved 'libllvm17t64_1%3a17.0.6-18_amd64.deb' to '/srv/rebuilderd/tmp/tmpmrul9i8p/libllvm17t64_17.0.6-18_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Fetched 47.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcw3hzx6o/libseccomp2_2.5.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgwzr6pm6/libevent-extra-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps5pj7wpa/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 ncurses-base all 6.5-2 [270 kB] Fetched 270 kB in 0s (25.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxg6n2o0t/ncurses-base_6.5-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libctf0 amd64 2.43.50.20241126-3 [88.4 kB] Fetched 88.4 kB in 0s (5249 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprxzp9n12/libctf0_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 tzdata all 2024b-3 [255 kB] Fetched 255 kB in 0s (2280 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmodikayx/tzdata_2024b-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzhcl8pgx/g++_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Fetched 287 kB in 0s (28.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm9me8z7j/m4_1.4.19-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-roman all 4.2-1 [10.4 kB] Fetched 10.4 kB in 0s (282 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp28pkvhz6/python3-roman_4.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dash amd64 0.5.12-9 [93.2 kB] Fetched 93.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpymv5hf0l/dash_0.5.12-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Fetched 40.6 kB in 0s (692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq36i0ymt/libnsl2_1.3.0-3+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Fetched 58.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjigwud46/librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Fetched 36.6 kB in 0s (1370 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5jl2ujmf/libnuma-dev_2.0.18-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Fetched 9280 B in 0s (347 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp958k5q_4/libatomic1_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB] Fetched 139 kB in 0s (8288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpju4z81m7/libsmartcols1_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Fetched 671 kB in 0s (4704 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb4bjkpp4/python3.12_3.12.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Fetched 61.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpra3dg909/libevent-openssl-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgfortran-14-dev amd64 14.2.0-8 [878 kB] Fetched 878 kB in 0s (10.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplce36guv/libgfortran-14-dev_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsemanage-common all 3.7-2 [7108 B] Fetched 7108 B in 0s (371 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcyrvn0j_/libsemanage-common_3.7-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libltdl-dev amd64 2.4.7-8 [165 kB] Fetched 165 kB in 0s (5920 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp21rtinv_/libltdl-dev_2.4.7-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Fetched 43.3 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.45-3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpvmm4n8v_/file_5.45-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Fetched 28.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_88pfesc/libcbor0.10_0.10.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b2 [560 kB] Fetched 560 kB in 0s (16.9 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmprwycpgue/libgmp10_6.3.0+dfsg-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Fetched 14.2 kB in 0s (627 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4mdjlzsa/libxnvctrl0_535.171.04-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Fetched 3836 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkb3rr4z_/libboost-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 binutils-x86-64-linux-gnu amd64 2.43.50.20241126-3 [2238 kB] Fetched 2238 kB in 0s (17.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprenh7cna/binutils-x86-64-linux-gnu_2.43.50.20241126-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo8vlmo6y/sed_4.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Fetched 535 kB in 0s (21.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprd3_wni0/libhsa-runtime64-1_6.1.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Fetched 724 kB in 0s (61.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd9uqpmz0/libmpfr6_4.2.1-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 login.defs all 1:4.16.0-5 [185 kB] Fetched 185 kB in 0s (1845 kB/s) dpkg-name: info: moved 'login.defs_1%3a4.16.0-5_all.deb' to '/srv/rebuilderd/tmp/tmps88nbqjq/login.defs_4.16.0-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Fetched 1205 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5fm1f09x/liblsan0_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Fetched 588 kB in 0s (8405 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcv91hmfx/python3-sphinx_7.4.7-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libattr1 amd64 1:2.5.2-2 [22.7 kB] Fetched 22.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpmzxmj4ny/libattr1_2.5.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 readline-common all 8.2-5 [69.3 kB] Fetched 69.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ech7phw/readline-common_8.2-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libc6-dev amd64 2.40-4 [1954 kB] Fetched 1954 kB in 0s (19.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdlq0rort/libc6-dev_2.40-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfh8is0gx/sensible-utils_0.0.24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8 [21.4 MB] Fetched 21.4 MB in 1s (35.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvn5pn8uo/gcc-14-x86-64-linux-gnu_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Fetched 25.9 kB in 0s (1346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2fqlukt/libitm1_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Fetched 50.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn70s8yi2/libgdbm-compat4t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Fetched 4840 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp805xzxco/cpp-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 man-db amd64 2.13.0-1 [1420 kB] Fetched 1420 kB in 0s (87.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_v3y95vd/man-db_2.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-babel all 2.16.0-1 [114 kB] Fetched 114 kB in 0s (4573 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcq3q09kn/python3-babel_2.16.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsprng2-dev amd64 2.0a-16 [78.8 kB] Fetched 78.8 kB in 0s (1841 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpje34erk2/libsprng2-dev_2.0a-16_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libc-dev-bin amd64 2.40-4 [52.0 kB] Fetched 52.0 kB in 0s (2131 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaakn8d0o/libc-dev-bin_2.40-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Fetched 32.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd1yp2gju/libkrb5support0_1.21.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Fetched 140 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpludq_0tr/libpam-runtime_1.5.3-7_all.deb' Downloading dependency 1 of 315: libamd-comgr2:amd64=6.0+git20231212.4510c28+dfsg-3+b2 Downloading dependency 2 of 315: python3-defusedxml:amd64=0.7.1-2 Downloading dependency 3 of 315: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b1 Downloading dependency 4 of 315: sgml-base:amd64=1.31 Downloading dependency 5 of 315: libidn2-0:amd64=2.3.7-2+b1 Downloading dependency 6 of 315: libelf1t64:amd64=0.192-4 Downloading dependency 7 of 315: libfile-stripnondeterminism-perl:amd64=1.14.0-1 Downloading dependency 8 of 315: libdrm2:amd64=2.4.123-1 Downloading dependency 9 of 315: grep:amd64=3.11-4 Downloading dependency 10 of 315: dpkg:amd64=1.22.11 Downloading dependency 11 of 315: libtirpc-common:amd64=1.3.4+ds-1.3 Downloading dependency 12 of 315: python3-typing-extensions:amd64=4.12.2-2 Downloading dependency 13 of 315: libxxhash0:amd64=0.8.2-2+b2 Downloading 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binutils-x86-64-linux-gnu:amd64=2.43.50.20241126-3 Downloading dependency 108 of 315: sed:amd64=4.9-2 Downloading dependency 109 of 315: libhsa-runtime64-1:amd64=6.1.2-2 Downloading dependency 110 of 315: libmpfr6:amd64=4.2.1-1+b2 Downloading dependency 111 of 315: login.defs:amd64=1:4.16.0-5 Downloading dependency 112 of 315: liblsan0:amd64=14.2.0-8 Downloading dependency 113 of 315: python3-sphinx:amd64=7.4.7-4 Downloading dependency 114 of 315: libattr1:amd64=1:2.5.2-2 Downloading dependency 115 of 315: readline-common:amd64=8.2-5 Downloading dependency 116 of 315: libc6-dev:amd64=2.40-4 Downloading dependency 117 of 315: sensible-utils:amd64=0.0.24 Downloading dependency 118 of 315: gcc-14-x86-64-linux-gnu:amd64=14.2.0-8 Downloading dependency 119 of 315: libitm1:amd64=14.2.0-8 Downloading dependency 120 of 315: libgdbm-compat4t64:amd64=1.24-2 Downloading dependency 121 of 315: cpp-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 122 of 315: man-db:amd64=2.13.0-1 Downloading dependency 123 of 315: python3-babel:amd64=2.16.0-1 Downloading dependency 124 of 315: libsprng2-dev:amd64=2.0a-16 Downloading dependency 125 of 315: libc-dev-bin:amd64=2.40-4 Downloading dependency 126 of 315: libkrb5support0:amd64=1.21.3-3 Downloading dependency 127 of 315: libpam-runtime:amd64=1.5.3-7 Downloading dependency 128 of 315: python3-charset-normalizer:amd64=3.4.0-1+b1Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Fetched 140 kB in 0s (4705 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuogku15p/python3-charset-normalizer_3.4.0-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnqba2qnq/hostname_3.25_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 usr-is-merged all 39 [5572 B] Fetched 5572 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8sgx412y/usr-is-merged_39_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Fetched 1130 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppt6v_ntx/libucx0_1.17.0+ds-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmount1 amd64 2.40.2-11 [199 kB] Fetched 199 kB in 0s (3503 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx324l094/libmount1_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Fetched 57.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ni7zujp/libpsl5t64_0.21.2-1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Fetched 10.1 kB in 0s (557 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp37hjghwy/libdebconfclient0_0.273_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 netbase all 6.4 [12.8 kB] Fetched 12.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptqcpfzc7/netbase_6.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhogweed6t64 amd64 3.10-1+b1 [335 kB] Fetched 335 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpslzbsgr0/libhogweed6t64_3.10-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmpgkjjr2la/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Fetched 9576 B in 0s (303 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4w2iehdk/python3-certifi_2024.8.30+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Fetched 200 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4b382ua8/gettext-base_0.22.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Fetched 836 kB in 0s (8544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj9hd30u4/python3-pygments_2.18.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libblkid1 amd64 2.40.2-11 [168 kB] Fetched 168 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6bbxzvke/libblkid1_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b1 [10.6 MB] Fetched 10.6 MB in 0s (58.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzd00c74f/libboost1.83-dev_1.83.0-3.2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpmix-dev amd64 5.0.4-1 [3972 kB] Fetched 3972 kB in 0s (46.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiawskn98/libpmix-dev_5.0.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Fetched 314 kB in 0s (29.2 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.45-3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpgc46svyc/libmagic-mgc_5.45-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Fetched 5696 kB in 0s (21.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjr9x4g5/python-babel-localedata_2.16.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Fetched 70.4 kB in 0s (1780 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphkeh7b9v/librdmacm1t64_52.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 procps amd64 2:4.0.4-6 [879 kB] Fetched 879 kB in 0s (14.5 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-6_amd64.deb' to '/srv/rebuilderd/tmp/tmpgyzc8sqs/procps_4.0.4-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsframe1 amd64 2.43.50.20241126-3 [77.3 kB] Fetched 77.3 kB in 0s (2844 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps5fh0zrc/libsframe1_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] Fetched 2271 kB in 0s (23.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6qqypao0/libssl3t64_3.3.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Fetched 2461 kB in 0s (72.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkpi7326n/libtsan2_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 bash amd64 5.2.32-1+b2 [1500 kB] Fetched 1500 kB in 0s (89.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6f1bytow/bash_5.2.32-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Fetched 72.7 kB in 0s (2254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1k8okld_/libgcc-s1_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Fetched 49.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp857xkwu1/libtasn1-6_4.19.0-3+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Fetched 51.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpowd3uw6m/autotools-dev_20220109.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Fetched 59.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmploo6izan/libhsakmt1_6.1.2+ds-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (24.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu6ct6gz4/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Fetched 2162 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps4qpe3r3/python3.12-minimal_3.12.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cpp-14 amd64 14.2.0-8 [1276 B] Fetched 1276 B in 0s (62.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzbnn7x7o/cpp-14_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libbsd0 amd64 0.12.2-2 [131 kB] Fetched 131 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpii97ijqq/libbsd0_0.12.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Fetched 58.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxad85cik/python3-snowballstemmer_2.2.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Fetched 30.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ew6zxvx/pkgconf-bin_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Fetched 9423 kB in 0s (59.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzv9wnwxo/libicu72_72.1-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Fetched 20.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplfjaxssw/libmunge2_0.5.15-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Fetched 20.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp6bb_1c49/libxau6_1.0.11-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 ca-certificates all 20240203 [158 kB] Fetched 158 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7h0pk4f/ca-certificates_20240203_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libselinux1 amd64 3.7-3+b1 [77.0 kB] Fetched 77.0 kB in 0s (7542 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptshjimwl/libselinux1_3.7-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Fetched 631 kB in 0s (11.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprablz3t6/libfabric1_1.17.0-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 debhelper all 13.20 [915 kB] Fetched 915 kB in 0s (73.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcdk15uto/debhelper_13.20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Fetched 8448 B in 0s (835 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpalx9njjj/dh-strip-nondeterminism_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdpkg-perl all 1.22.11 [644 kB] Fetched 644 kB in 0s (59.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpziw6pt6k/libdpkg-perl_1.22.11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Fetched 79.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj_cihys1/libk5crypto3_1.21.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Fetched 991 kB in 0s (13.6 MB/s) dpkg-name: info: moved 'openssh-client_1%3a9.9p1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpuu2x_93f/openssh-client_9.9p1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Fetched 50.5 kB in 0s (1955 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpz_7iw_yv/libxext6_1.3.4-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Fetched 1489 kB in 0s (11.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyuon_vo1/libhwasan0_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsystemd0 amd64 257~rc2-3 [447 kB] Fetched 447 kB in 0s (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4cbz9n0s/libsystemd0_257~rc2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 g++-14 amd64 14.2.0-8 [20.2 kB] Fetched 20.2 kB in 0s (1260 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1nfq978l/g++-14_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Fetched 47.2 kB in 0s (1904 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphvz6q_z8/gcc-14-base_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Fetched 62.2 kB in 0s (2964 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprdu20o7w/libibverbs1_52.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1en3qqdf/python3-imagesize_1.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 920 kB in 0s (53.6 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpq1q_jc5_/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Fetched 337 kB in 0s (0 B/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.10-2_all.deb' to '/srv/rebuilderd/tmp/tmpzzhrbe7w/libx11-data_1.8.10-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4jh504_p/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 liblz4-1 amd64 1.9.4-3+b1 [60.3 kB] Fetched 60.3 kB in 0s (1346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn2nayn03/liblz4-1_1.9.4-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Fetched 88.9 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpg917u0zz/zlib1g_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Fetched 169 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphe9zfths/libreadline8t64_8.2-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgprofng0 amd64 2.43.50.20241126-3 [807 kB] Fetched 807 kB in 0s (31.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7kkckg9v/libgprofng0_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 patch amd64 2.7.6-7 [128 kB] Fetched 128 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj6rwryqj/patch_2.7.6-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Fetched 699 kB in 0s (63.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7z_5smle/libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Fetched 13.9 kB in 0s (850 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn0p2ugqu/python3-markupsafe_2.1.5-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Fetched 91.5 kB in 0s (2055 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp41ovddpr/bsdextrautils_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Fetched 4320 kB in 0s (149 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpry8j89p6/libperl5.40_5.40.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Fetched 37.0 kB in 0s (1683 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2n7qn_91/python3-typeguard_4.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Fetched 22.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7g7ph4qt/libnuma1_2.0.18-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Fetched 813 kB in 0s (69.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnde0t_mh/tar_1.35+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 mawk amd64 1.3.4.20240905-1 [138 kB] Fetched 138 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbtdkx4sq/mawk_1.3.4.20240905-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 util-linux amd64 2.40.2-11 [1213 kB] Fetched 1213 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpum62n5kq/util-linux_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: info: moved 'bsdutils_1%3a2.40.2-11_amd64.deb' to '/srv/rebuilderd/tmp/tmpv4f115xm/bsdutils_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpmix2t64 amd64 5.0.4-1 [661 kB] Fetched 661 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkvh46893/libpmix2t64_5.0.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Fetched 40.2 kB in 0s (1876 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprxc4az6h/ocl-icd-libopencl1_2.3.2-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq7d9p_bc/libacl1_2.3.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Fetched 13.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5ki_8u3/chrpath_0.18-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libp11-kit0 amd64 0.25.5-2+b1 [429 kB] Fetched 429 kB in 0s (3694 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdxler1y5/libp11-kit0_0.25.5-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Fetched 89.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc7n06f15/libdebhelper-perl_13.20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Fetched 393 kB in 0s (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkks86dh/libltdl7_2.4.7-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Fetched 9712 B in 0s (321 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0710jnik/libpython3-stdlib_3.12.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libunistring5 amd64 1.2-1+b1 [429 kB] Fetched 429 kB in 0s (19.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptdnvnqxp/libunistring5_1.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Fetched 145 kB in 0s (5539 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi0tgsuh1/libquadmath0_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB] Fetched 35.9 kB in 0s (1551 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc6f93jhr/libuuid1_2.40.2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 perl amd64 5.40.0-8 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl6_pehbm/perl_5.40.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cmake-data all 3.31.1-1 [2267 kB] Fetched 2267 kB in 0s (35.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgop_hamm/cmake-data_3.31.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxn0m9uy3/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB] Fetched 54.9 kB in 0s (3158 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpm5mzo426/libaudit1_4.0.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 base-passwd amd64 3.6.5 [53.1 kB] Fetched 53.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgg7l66tu/base-passwd_3.6.5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 debconf all 1.5.87 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cjsmyjb/debconf_1.5.87_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Fetched 1454 kB in 0s (99.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxnsk8ci7/libgnutls30t64_3.8.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 mpi-default-dev amd64 1.17 [3148 B] Fetched 3148 B in 0s (177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp397d4wi_/mpi-default-dev_1.17_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Fetched 137 kB in 0s (3505 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0xaesejx/libgomp1_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8 [11.7 MB] Fetched 11.7 MB in 0s (44.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7o_sgn39/gfortran-14-x86-64-linux-gnu_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8 [11.1 MB] Fetched 11.1 MB in 0s (45.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpphq0ggd2/cpp-14-x86-64-linux-gnu_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Fetched 26.8 kB in 0s (1098 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwg1rbnpk/python3-minimal_3.12.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 autoconf all 2.72-3 [493 kB] Fetched 493 kB in 0s (46.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdt5cqb5m/autoconf_2.72-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Fetched 19.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_s29rtmc/libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpma78xo3d/libxcb1_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 binutils amd64 2.43.50.20241126-3 [68.1 kB] Fetched 68.1 kB in 0s (1779 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgvefw8ad/binutils_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3crym2fj/libncursesw6_6.5-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 sysvinit-utils amd64 3.11-1 [33.1 kB] Fetched 33.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw9ew7jbv/sysvinit-utils_3.11-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Fetched 626 kB in 0s (6770 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf37zhmf_/libc-bin_2.40-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 debianutils amd64 5.21 [92.1 kB] Fetched 92.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmk9wrtg4/debianutils_5.21_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Fetched 642 kB in 0s (23.4 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpjfk72fme/libgmp-dev_6.3.0+dfsg-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241202T150356Z sid/main amd64 openmpi-bin amd64 5.0.6-2 [189 kB] Fetched 189 kB in 0s (4363 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphsou2ml5/openmpi-bin_5.0.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Fetched 32.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpofo41ek5/python3-inflect_7.3.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Fetched 375 kB in 0s (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.10-1_amd64.deb' to '/srv/rebuilderd/tmp/tmps2y9eiei/diffutils_3.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Fetched 8560 kB in 0s (178 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9949zd1m/libz3-4_4.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 make amd64 4.3-4.1 [396 kB] Fetched 396 kB in 0s (36.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplh2t3uby/make_4.3-4.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Fetched 636 kB in 0s (15.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph2dl4jyt/libibverbs-dev_52.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 openssl amd64 3.3.2-2 [1382 kB] Fetched 1382 kB in 0s (16.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7yu4n3dt/openssl_3.3.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Fetched 43.4 kB in 0s (874 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgywkqlsc/libibmad5_52.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 passwd amd64 1:4.16.0-5 [1232 kB] Fetched 1232 kB in 0s (24.8 MB/s) dpkg-name: info: moved 'passwd_1%3a4.16.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpvnkx2cim/passwd_4.16.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Fetched 18.1 kB in 0s (1057 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp84yyoavt/libhwloc-plugins_2.11.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 media-types all 10.1.0 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8n7l975w/media-types_10.1.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8 [12.1 MB] Fetched 12.1 MB in 0s (65.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9_4lv222/g++-14-x86-64-linux-gnu_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpam0g amd64 1.5.3-7+b1 [68.3 kB] Fetched 68.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8a7tc1d9/libpam0g_1.5.3-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Fetched 5136 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxllum5ls/gcc_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Fetched 813 kB in 0s (52.3 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.10-2_amd64.deb' to '/srv/rebuilderd/tmp/tmp995fpkyc/libx11-6_1.8.10-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjmb0jjbl/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Fetched 83.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgk7o9zni/libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwig9nztd/build-essential_12.12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Fetched 78.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnd14jsnd/libfido2-1_1.15.0-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Fetched 118 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.36-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpgm_l0w9t/libcrypt-dev_4.4.36-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Fetched 1041 kB in 0s (9709 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgimcnz0y/libeigen3-dev_3.4.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Fetched 329 kB in 0s (12.5 MB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpdrr6axig/libgmpxx4ldbl_6.3.0+dfsg-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Fetched 75.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvu36p6hd/libnghttp2-14_1.64.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Fetched 349 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ik18vdn/libarchive13t64_3.7.4-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Fetched 55.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvtp_1sk8/python3-packaging_24.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1tztym7c/libjson-perl_4.10000-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Fetched 302 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9999si_e/libbrotli1_1.1.0-2+b6_amd64.deb' Downloading dependency 129 of 315: hostname:amd64=3.25 Downloading dependency 130 of 315: usr-is-merged:amd64=39 Downloading dependency 131 of 315: libucx0:amd64=1.17.0+ds-3 Downloading dependency 132 of 315: libmount1:amd64=2.40.2-11 Downloading dependency 133 of 315: libpsl5t64:amd64=0.21.2-1.1+b1 Downloading dependency 134 of 315: libdebconfclient0:amd64=0.273 Downloading dependency 135 of 315: netbase:amd64=6.4 Downloading dependency 136 of 315: libhogweed6t64:amd64=3.10-1+b1 Downloading dependency 137 of 315: libaudit-common:amd64=1:4.0.2-2 Downloading dependency 138 of 315: python3-certifi:amd64=2024.8.30+dfsg-1 Downloading dependency 139 of 315: gettext-base:amd64=0.22.5-2 Downloading dependency 140 of 315: python3-pygments:amd64=2.18.0+dfsg-1 Downloading dependency 141 of 315: libblkid1:amd64=2.40.2-11 Downloading dependency 142 of 315: libboost1.83-dev:amd64=1.83.0-3.2+b1 Downloading dependency 143 of 315: libpmix-dev:amd64=5.0.4-1 Downloading dependency 144 of 315: libmagic-mgc:amd64=1:5.45-3+b1 Downloading dependency 145 of 315: python-babel-localedata:amd64=2.16.0-1 Downloading dependency 146 of 315: librdmacm1t64:amd64=52.0-2+b1 Downloading dependency 147 of 315: procps:amd64=2:4.0.4-6 Downloading dependency 148 of 315: libsframe1:amd64=2.43.50.20241126-3 Downloading dependency 149 of 315: libssl3t64:amd64=3.3.2-2 Downloading dependency 150 of 315: libtsan2:amd64=14.2.0-8 Downloading dependency 151 of 315: bash:amd64=5.2.32-1+b2 Downloading dependency 152 of 315: libgcc-s1:amd64=14.2.0-8 Downloading dependency 153 of 315: libtasn1-6:amd64=4.19.0-3+b3 Downloading dependency 154 of 315: autotools-dev:amd64=20220109.1 Downloading dependency 155 of 315: libhsakmt1:amd64=6.1.2+ds-1 Downloading dependency 156 of 315: po-debconf:amd64=1.0.21+nmu1 Downloading dependency 157 of 315: python3.12-minimal:amd64=3.12.7-3 Downloading dependency 158 of 315: cpp-14:amd64=14.2.0-8 Downloading dependency 159 of 315: libbsd0:amd64=0.12.2-2 Downloading dependency 160 of 315: python3-snowballstemmer:amd64=2.2.0-4 Downloading dependency 161 of 315: pkgconf-bin:amd64=1.8.1-4 Downloading dependency 162 of 315: libicu72:amd64=72.1-5+b1 Downloading dependency 163 of 315: libmunge2:amd64=0.5.15-4+b1 Downloading dependency 164 of 315: libxau6:amd64=1:1.0.11-1 Downloading dependency 165 of 315: ca-certificates:amd64=20240203 Downloading dependency 166 of 315: libselinux1:amd64=3.7-3+b1 Downloading dependency 167 of 315: libfabric1:amd64=1.17.0-3.1 Downloading dependency 168 of 315: debhelper:amd64=13.20 Downloading dependency 169 of 315: dh-strip-nondeterminism:amd64=1.14.0-1 Downloading dependency 170 of 315: libdpkg-perl:amd64=1.22.11 Downloading dependency 171 of 315: libk5crypto3:amd64=1.21.3-3 Downloading dependency 172 of 315: openssh-client:amd64=1:9.9p1-3 Downloading dependency 173 of 315: libxext6:amd64=2:1.3.4-1+b2 Downloading dependency 174 of 315: libhwasan0:amd64=14.2.0-8 Downloading dependency 175 of 315: libsystemd0:amd64=257~rc2-3 Downloading dependency 176 of 315: g++-14:amd64=14.2.0-8 Downloading dependency 177 of 315: gcc-14-base:amd64=14.2.0-8 Downloading dependency 178 of 315: libibverbs1:amd64=52.0-2+b1 Downloading dependency 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dependency 225 of 315: libncursesw6:amd64=6.5-2+b1 Downloading dependency 226 of 315: sysvinit-utils:amd64=3.11-1 Downloading dependency 227 of 315: libc-bin:amd64=2.40-4 Downloading dependency 228 of 315: debianutils:amd64=5.21 Downloading dependency 229 of 315: libgmp-dev:amd64=2:6.3.0+dfsg-2+b2 Downloading dependency 230 of 315: openmpi-bin:amd64=5.0.6-2 Downloading dependency 231 of 315: python3-inflect:amd64=7.3.1-2 Downloading dependency 232 of 315: diffutils:amd64=1:3.10-1 Downloading dependency 233 of 315: libz3-4:amd64=4.13.3-1 Downloading dependency 234 of 315: make:amd64=4.3-4.1 Downloading dependency 235 of 315: libibverbs-dev:amd64=52.0-2+b1 Downloading dependency 236 of 315: openssl:amd64=3.3.2-2 Downloading dependency 237 of 315: libibmad5:amd64=52.0-2+b1 Downloading dependency 238 of 315: passwd:amd64=1:4.16.0-5 Downloading dependency 239 of 315: libhwloc-plugins:amd64=2.11.2-1 Downloading dependency 240 of 315: media-types:amd64=10.1.0 Downloading dependency 241 of 315: g++-14-x86-64-linux-gnu:amd64=14.2.0-8 Downloading dependency 242 of 315: libpam0g:amd64=1.5.3-7+b1 Downloading dependency 243 of 315: gcc:amd64=4:14.2.0-1 Downloading dependency 244 of 315: libx11-6:amd64=2:1.8.10-2 Downloading dependency 245 of 315: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 246 of 315: libtirpc3t64:amd64=1.3.4+ds-1.3+b1 Downloading dependency 247 of 315: build-essential:amd64=12.12 Downloading dependency 248 of 315: libfido2-1:amd64=1.15.0-1+b1 Downloading dependency 249 of 315: libcrypt-dev:amd64=1:4.4.36-5 Downloading dependency 250 of 315: libeigen3-dev:amd64=3.4.0-4 Downloading dependency 251 of 315: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-2+b2 Downloading dependency 252 of 315: libnghttp2-14:amd64=1.64.0-1 Downloading dependency 253 of 315: libarchive13t64:amd64=3.7.4-1.1 Downloading dependency 254 of 315: python3-packaging:amd64=24.2-1 Downloading dependency 255 of 315: libjson-perl:amd64=4.10000-1 Downloading dependency 256 of 315: libbrotli1:amd64=1.1.0-2+b6 Downloading dependency 257 of 315: libproc2-0:amd64=2:4.0.4-6Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Fetched 64.8 kB in 0s (1576 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-6_amd64.deb' to '/srv/rebuilderd/tmp/tmp53brk0bs/libproc2-0_4.0.4-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 binutils-common amd64 2.43.50.20241126-3 [2628 kB] Fetched 2628 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_s6q1w7/binutils-common_2.43.50.20241126-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Fetched 13.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsird0r_q/python3-autocommand_2.2.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libtinfo6 amd64 6.5-2+b1 [344 kB] Fetched 344 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7106ma_3/libtinfo6_6.5-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 ncurses-bin amd64 6.5-2+b1 [434 kB] Fetched 434 kB in 0s (43.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1cjm4ht7/ncurses-bin_6.5-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Fetched 63.8 kB in 0s (1654 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvsrcjb0t/python3-more-itertools_10.5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Fetched 182 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt9vhtqs_/libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Fetched 351 kB in 0s (9480 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfhxo3f8j/libcurl4t64_8.11.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Fetched 15.3 kB in 0s (968 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprfp51h31/liblocale-gettext-perl_1.07-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsepol2 amd64 3.7-1 [293 kB] Fetched 293 kB in 0s (9856 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvhordbhw/libsepol2_3.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Fetched 93.9 kB in 0s (4530 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6nomulx6/libedit2_3.1-20240808-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Fetched 75.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvv_seu8k/libgdbm6t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Fetched 36.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsea5kx2x/libpkgconf3_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Fetched 111 kB in 0s (2904 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7jwhfl72/python3-urllib3_2.0.7-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 xz-utils amd64 5.6.3-1+b1 [542 kB] Fetched 542 kB in 0s (51.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6fb9u6v7/xz-utils_5.6.3-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Fetched 2922 kB in 0s (134 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkjd0jupx/coreutils_9.5-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libudev1 amd64 257~rc2-3 [147 kB] Fetched 147 kB in 0s (8053 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7dsqk81k/libudev1_257~rc2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0lcnm082/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Fetched 100 kB in 0s (2799 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvwxxz0l5/libnl-3-dev_3.7.0-0.3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 26.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl17snqw4/pkgconf_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Fetched 68.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph5ngvktx/libuchardet0_0.0.8-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Fetched 23.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp244o8afs/libffi8_3.4.6-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Fetched 106 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplm3w_4mp/libexpat1_2.6.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Fetched 403 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8micngcu/python3-docutils_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Fetched 1075 kB in 0s (16.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwlirt_km/libubsan1_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Fetched 148 kB in 0s (3397 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptmd9wn9l/libuv1t64_1.48.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Fetched 714 kB in 0s (9000 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0tylb2o7/libstdc++6_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libsprng2 amd64 2.0a-16 [76.4 kB] Fetched 76.4 kB in 0s (2157 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc8hwm5i5/libsprng2_2.0a-16_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptt1jlanh/libgssapi-krb5-2_1.21.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Fetched 343 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj9eah1sb/ibverbs-providers_52.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libisl23 amd64 0.27-1 [659 kB] Fetched 659 kB in 0s (59.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnba6dhs_/libisl23_0.27-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Fetched 81.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm79u3b2f/libjsoncpp26_1.9.6-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gfortran-14 amd64 14.2.0-8 [12.2 kB] Fetched 12.2 kB in 0s (1041 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_a95zatl/gfortran-14_14.2.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp703hmtpb/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Fetched 254 kB in 0s (7533 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpolyc_pm8/libhwloc-dev_2.11.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 liblzma5 amd64 5.6.3-1+b1 [272 kB] Fetched 272 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwuw5tjg/liblzma5_5.6.3-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Fetched 823 kB in 0s (71.4 MB/s) dpkg-name: info: moved 'automake_1%3a1.16.5-1.3_all.deb' to '/srv/rebuilderd/tmp/tmpjybrc6o8/automake_1.16.5-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libdrm-common all 2.4.123-1 [8084 B] Fetched 8084 B in 0s (120 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsenlnjyu/libdrm-common_2.4.123-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Fetched 27.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpwdbcwrkg/libxdmcp6_1.1.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Fetched 71.9 kB in 0s (3422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfrm62ze5/python3-requests_2.32.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-idna all 3.8-2 [41.6 kB] Fetched 41.6 kB in 0s (1631 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpftd0uvj9/python3-idna_3.8-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxfhowxvu/gcc-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Fetched 3015 kB in 0s (134 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplisy082u/perl-modules-5.40_5.40.0-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2w9chmi7/libmpc3_1.3.1-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpt3drodgg/g++-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dwz amd64 0.15-1+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_bu1xd7/dwz_0.15-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Fetched 836 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_7um6sr7/libgfortran5_14.2.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Fetched 107 kB in 0s (4011 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppv38iyx1/python3-chardet_5.2.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241202T150356Z sid/main amd64 libopenmpi-dev amd64 5.0.6-2 [1088 kB] Fetched 1088 kB in 0s (16.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ev9hpc1/libopenmpi-dev_5.0.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Fetched 28.2 kB in 0s (1174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmlmrf2la/libibumad3_52.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 cmake amd64 3.31.1-1 [11.9 MB] Fetched 11.9 MB in 1s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuwcxa827/cmake_3.31.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Fetched 39.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjgr9u1_h/libjansson4_2.14-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libpam-modules-bin amd64 1.5.3-7+b1 [54.1 kB] Fetched 54.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpic3oxx45/libpam-modules-bin_1.5.3-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Fetched 1181 kB in 0s (90.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kvkezlo/groff-base_1.23.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvxkzz1j6/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Fetched 158 kB in 0s (4752 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmkds7nun/libjs-sphinxdoc_7.4.7-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Fetched 23.2 kB in 0s (1047 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy8f367fx/libcom-err2_1.47.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcyjdr3u/bzip2_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241127T204405Z sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Fetched 245 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5nqrzzwc/libssh2-1t64_1.11.1-1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpegyj92wf/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza 127.0.0.1 - - [02/Mar/2026 10:04:33] code 404, message File not found 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41215 ./ InRelease 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:41215 ./ Release [462 B] 127.0.0.1 - - [02/Mar/2026 10:04:33] code 404, message File not found 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41215 ./ Release.gpg 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:41215 ./ Packages [393 kB] Fetched 394 kB in 0s (24.8 MB/s) Reading package lists... usr-is-merged found -- running merged-usr setup hook dpkg-deb: building package 'usr-is-merged' in '/srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/tmp/tmp.zvdG9SUEla/usr-is-merged.deb'. Selecting previously unselected package usr-is-merged. (Reading database ... 0 files and directories currently installed.) Preparing to unpack .../usr-is-merged.deb ... Unpacking usr-is-merged (1) ... touch: cannot touch '/run/needrestart/unpacked': Permission denied Setting up usr-is-merged (1) ... I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./gcc-14-base_14.2.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libc6_2.40-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libgcc-s1_14.2.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./mawk_1.3.4.20240905-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./base-files_13.6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libtinfo6_6.5-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./debianutils_5.21_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./bash_5.2.32-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libcap2_2.66-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libsystemd0_257%7erc2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./bsdutils_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libacl1_2.3.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libattr1_2.5.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libgmp10_6.3.0%2bdfsg-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:33] "GET /./libpcre2-8-0_10.44-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libselinux1_3.7-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libzstd1_1.5.6%2bdfsg-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libssl3t64_3.3.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./openssl-provider-legacy_3.3.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./coreutils_9.5-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./dash_0.5.12-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./diffutils_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libbz2-1.0_1.0.8-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./liblzma5_5.6.3-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libmd0_1.1.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./tar_1.35%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./dpkg_1.22.11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./grep_3.11-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./gzip_1.12-1.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./ncurses-bin_6.5-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libcrypt1_4.4.36-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./perl-base_5.40.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libaudit-common_4.0.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libcap-ng0_0.8.5-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libaudit1_4.0.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libdb5.3t64_5.3.28%2bdfsg2-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./debconf_1.5.87_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libpam0g_1.5.3-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libpam-modules-bin_1.5.3-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libpam-modules_1.5.3-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libpam-runtime_1.5.3-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libblkid1_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libmount1_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libsmartcols1_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libudev1_257%7erc2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libuuid1_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./util-linux_2.40.2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libdebconfclient0_0.273_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./base-passwd_3.6.5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./init-system-helpers_1.67_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./libc-bin_2.40-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./ncurses-base_6.5-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:34] "GET /./sysvinit-utils_3.11-1_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza 127.0.0.1 - - [02/Mar/2026 10:04:35] code 404, message File not found 127.0.0.1 - - [02/Mar/2026 10:04:35] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41215 ./ InRelease 127.0.0.1 - - [02/Mar/2026 10:04:35] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:41215 ./ Release 127.0.0.1 - - [02/Mar/2026 10:04:35] code 404, message File not found 127.0.0.1 - - [02/Mar/2026 10:04:35] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41215 ./ Release.gpg Reading package lists... usr-is-merged found -- running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza dummy usr-is-merged package installed -- running merged-usr essential hook Reading package lists... Building dependency tree... The following packages will be upgraded: usr-is-merged 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./usr-is-merged_39_all.deb HTTP/1.1" 200 - 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5572 B of archives. After this operation, 13.3 kB of additional disk space will be used. Get:1 http://localhost:41215 ./ usr-is-merged 39 [5572 B] Fetched 5572 B in 0s (0 B/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/ (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 3537 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (1) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/ Setting up usr-is-merged (39) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/ I: installing remaining packages inside the chroot... 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./liblocale-gettext-perl_1.07-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./libpython3.12-minimal_3.12.7-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./libexpat1_2.6.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./python3.12-minimal_3.12.7-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./python3-minimal_3.12.7-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./media-types_10.1.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./netbase_6.4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./tzdata_2024b-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./libffi8_3.4.6-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:48] "GET /./libncursesw6_6.5-2%2bb1_amd64.deb HTTP/1.1" 200 - 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- [02/Mar/2026 10:04:50] "GET /./python3-snowballstemmer_2.2.0-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./python3-sphinx_7.4.7-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libsprng2_2.0a-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libgmpxx4ldbl_6.3.0%2bdfsg-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libgmp-dev_6.3.0%2bdfsg-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libsprng2-dev_2.0a-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libhwloc-dev_2.11.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libpmix-dev_5.0.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./gfortran-14-x86-64-linux-gnu_14.2.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./gfortran-14_14.2.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libibverbs-dev_52.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./openmpi-bin_5.0.6-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libopenmpi-dev_5.0.6-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./mpi-default-dev_1.17_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./libeigen3-dev_3.4.0-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Mar/2026 10:04:50] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpegyj92wf/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza Reading package lists... Building dependency tree... Reading state information... libamd-comgr2 is already the newest version (6.0+git20231212.4510c28+dfsg-3+b2). libamd-comgr2 set to manually installed. python3-defusedxml is already the newest version (0.7.1-2). python3-defusedxml set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-pthreads-2.1-7t64 set to manually installed. sgml-base is already the newest version (1.31). sgml-base set to manually installed. libidn2-0 is already the newest version (2.3.7-2+b1). libidn2-0 set to manually installed. libelf1t64 is already the newest version (0.192-4). libelf1t64 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.14.0-1). libfile-stripnondeterminism-perl set to manually installed. libdrm2 is already the newest version (2.4.123-1). libdrm2 set to manually installed. grep is already the newest version (3.11-4). dpkg is already the newest version (1.22.11). libtirpc-common is already the newest version (1.3.4+ds-1.3). libtirpc-common set to manually installed. python3-typing-extensions is already the newest version (4.12.2-2). python3-typing-extensions set to manually installed. libxxhash0 is already the newest version (0.8.2-2+b2). libxxhash0 set to manually installed. python3-jinja2 is already the newest version (3.1.3-1). python3-jinja2 set to manually installed. libnl-route-3-200 is already the newest version (3.7.0-0.3+b1). libnl-route-3-200 set to manually installed. libpython3.12-minimal is already the newest version (3.12.7-3). libpython3.12-minimal set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). time is already the newest version (1.9-0.2). time set to manually installed. gettext is already the newest version (0.22.5-2). gettext set to manually installed. libldap-2.5-0 is already the newest version (2.5.18+dfsg-3+b1). libldap-2.5-0 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6). libc6 is already the newest version (2.40-4). libgcc-14-dev is already the newest version (14.2.0-8). libgcc-14-dev set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-8). libstdc++-14-dev set to manually installed. libtool is already the newest version (2.4.7-8). libtool set to manually installed. libbinutils is already the newest version (2.43.50.20241126-3). libbinutils set to manually installed. dpkg-dev is already the newest version (1.22.11). dpkg-dev set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-8). libsasl2-2 set to manually installed. libpam-modules is already the newest version (1.5.3-7+b1). cpp is already the newest version (4:14.2.0-1). cpp set to manually installed. openssl-provider-legacy is already the newest version (3.3.2-2). openmpi-common is already the newest version (5.0.6-2). openmpi-common set to manually installed. libmagic1t64 is already the newest version (1:5.45-3+b1). libmagic1t64 set to manually installed. init-system-helpers is already the newest version (1.67). libpython3.12-stdlib is already the newest version (3.12.7-3). libpython3.12-stdlib set to manually installed. libasan8 is already the newest version (14.2.0-8). libasan8 set to manually installed. libcap2 is already the newest version (1:2.66-5+b1). gzip is already the newest version (1.12-1.1). libjs-underscore is already the newest version (1.13.4~dfsg+~1.11.4-3). libjs-underscore set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-core-2.1-7t64 set to manually installed. libpcre2-8-0 is already the newest version (10.44-4). libnettle8t64 is already the newest version (3.10-1+b1). libnettle8t64 set to manually installed. perl-base is already the newest version (5.40.0-8). libcap-ng0 is already the newest version (0.8.5-3+b1). libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. libkeyutils1 is already the newest version 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libjs-jquery set to manually installed. libllvm17t64 is already the newest version (1:17.0.6-18). libllvm17t64 set to manually installed. libseccomp2 is already the newest version (2.5.5-2). libseccomp2 set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-extra-2.1-7t64 set to manually installed. python3-alabaster is already the newest version (0.7.16-0.1). python3-alabaster set to manually installed. ncurses-base is already the newest version (6.5-2). libctf0 is already the newest version (2.43.50.20241126-3). libctf0 set to manually installed. tzdata is already the newest version (2024b-3). tzdata set to manually installed. g++ is already the newest version (4:14.2.0-1). g++ set to manually installed. m4 is already the newest version (1.4.19-4). m4 set to manually installed. python3-roman is already the newest version (4.2-1). python3-roman set to manually installed. dash is already the newest version (0.5.12-9). libnsl2 is 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(7.4.7-4). python3-sphinx set to manually installed. libattr1 is already the newest version (1:2.5.2-2). readline-common is already the newest version (8.2-5). readline-common set to manually installed. libc6-dev is already the newest version (2.40-4). libc6-dev set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. gcc-14-x86-64-linux-gnu is already the newest version (14.2.0-8). gcc-14-x86-64-linux-gnu set to manually installed. libitm1 is already the newest version (14.2.0-8). libitm1 set to manually installed. libgdbm-compat4t64 is already the newest version (1.24-2). libgdbm-compat4t64 set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:14.2.0-1). cpp-x86-64-linux-gnu set to manually installed. man-db is already the newest version (2.13.0-1). man-db set to manually installed. python3-babel is already the newest version (2.16.0-1). python3-babel set to manually installed. libsprng2-dev is already the newest version (2.0a-16). libsprng2-dev set to manually installed. libc-dev-bin is already the newest version (2.40-4). libc-dev-bin set to manually installed. libkrb5support0 is already the newest version (1.21.3-3). libkrb5support0 set to manually installed. libpam-runtime is already the newest version (1.5.3-7). python3-charset-normalizer is already the newest version (3.4.0-1+b1). python3-charset-normalizer set to manually installed. hostname is already the newest version (3.25). usr-is-merged is already the newest version (39). libucx0 is already the newest version (1.17.0+ds-3). libucx0 set to manually installed. libmount1 is already the newest version (2.40.2-11). libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. libdebconfclient0 is already the newest version (0.273). netbase is already the newest version (6.4). netbase set to manually installed. libhogweed6t64 is already the newest version (3.10-1+b1). libhogweed6t64 set to manually installed. libaudit-common is already the newest version (1:4.0.2-2). python3-certifi is already the newest version (2024.8.30+dfsg-1). python3-certifi set to manually installed. gettext-base is already the newest version (0.22.5-2). gettext-base set to manually installed. python3-pygments is already the newest version (2.18.0+dfsg-1). python3-pygments set to manually installed. libblkid1 is already the newest version (2.40.2-11). libboost1.83-dev is already the newest version (1.83.0-3.2+b1). libboost1.83-dev set to manually installed. libpmix-dev is already the newest version (5.0.4-1). libpmix-dev set to manually installed. libmagic-mgc is already the newest version (1:5.45-3+b1). libmagic-mgc set to manually installed. python-babel-localedata is already the newest version (2.16.0-1). python-babel-localedata set to manually installed. librdmacm1t64 is already the newest version (52.0-2+b1). librdmacm1t64 set to manually installed. procps is already the newest version (2:4.0.4-6). procps set to manually installed. libsframe1 is already the newest version (2.43.50.20241126-3). libsframe1 set to manually installed. libssl3t64 is already the newest version (3.3.2-2). libtsan2 is already the newest version (14.2.0-8). libtsan2 set to manually installed. bash is already the newest version (5.2.32-1+b2). libgcc-s1 is already the newest version (14.2.0-8). libtasn1-6 is already the newest version (4.19.0-3+b3). libtasn1-6 set to manually installed. autotools-dev is already the newest version (20220109.1). autotools-dev set to manually installed. libhsakmt1 is already the newest version (6.1.2+ds-1). libhsakmt1 set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. python3.12-minimal is already the newest version (3.12.7-3). python3.12-minimal set to manually installed. cpp-14 is already the newest version (14.2.0-8). cpp-14 set to manually installed. libbsd0 is already the newest version (0.12.2-2). libbsd0 set to manually installed. python3-snowballstemmer is already the newest version (2.2.0-4). python3-snowballstemmer set to manually installed. pkgconf-bin is already the newest version (1.8.1-4). pkgconf-bin set to manually installed. libicu72 is already the newest version (72.1-5+b1). libicu72 set to manually installed. libmunge2 is already the newest version (0.5.15-4+b1). libmunge2 set to manually installed. libxau6 is already the newest version (1:1.0.11-1). libxau6 set to manually installed. ca-certificates is already the newest version (20240203). ca-certificates set to manually installed. libselinux1 is already the newest version (3.7-3+b1). libfabric1 is already the newest version (1.17.0-3.1). libfabric1 set to manually installed. debhelper is already the newest version (13.20). debhelper set to manually installed. dh-strip-nondeterminism is already the newest version (1.14.0-1). dh-strip-nondeterminism set to manually installed. libdpkg-perl is already the newest version (1.22.11). libdpkg-perl set to manually installed. libk5crypto3 is already the newest version (1.21.3-3). libk5crypto3 set to manually installed. openssh-client is already the newest version (1:9.9p1-3). openssh-client set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b2). libxext6 set to manually installed. libhwasan0 is already the newest version (14.2.0-8). libhwasan0 set to manually installed. libsystemd0 is already the newest version (257~rc2-3). g++-14 is already the newest version (14.2.0-8). g++-14 set to manually installed. gcc-14-base is already the newest version (14.2.0-8). libibverbs1 is already the newest version (52.0-2+b1). libibverbs1 set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. libx11-data is already the newest version (2:1.8.10-2). libx11-data set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. liblz4-1 is already the newest version (1.9.4-3+b1). liblz4-1 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). libreadline8t64 is already the newest version (8.2-5). libreadline8t64 set to manually installed. libgprofng0 is already the newest version (2.43.50.20241126-3). libgprofng0 set to manually installed. patch is already the newest version (2.7.6-7). patch set to manually installed. libxml2 is already the newest version (2.12.7+dfsg+really2.9.14-0.2+b1). libxml2 set to manually installed. python3-markupsafe is already the newest version (2.1.5-1+b2). python3-markupsafe set to manually installed. bsdextrautils is already the newest version (2.40.2-11). bsdextrautils set to manually installed. libperl5.40 is already the newest version (5.40.0-8). libperl5.40 set to manually installed. python3-typeguard is already the newest version (4.4.1-1). python3-typeguard set to manually installed. libnuma1 is already the newest version (2.0.18-1+b1). libnuma1 set to manually installed. tar is already the newest version (1.35+dfsg-3). mawk is already the newest version (1.3.4.20240905-1). util-linux is already the newest version (2.40.2-11). bsdutils is already the newest version (1:2.40.2-11). libpmix2t64 is already the newest version (5.0.4-1). libpmix2t64 set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.2-1+b2). ocl-icd-libopencl1 set to manually installed. libacl1 is already the newest version (2.3.2-2+b1). chrpath is already the newest version (0.18-1). chrpath set to manually installed. libp11-kit0 is already the newest version (0.25.5-2+b1). libp11-kit0 set to manually installed. libdebhelper-perl is already the newest version (13.20). libdebhelper-perl set to manually installed. libltdl7 is already the newest version (2.4.7-8). libltdl7 set to manually installed. libpython3-stdlib is already the newest version (3.12.7-1). libpython3-stdlib set to manually installed. libunistring5 is already the newest version (1.2-1+b1). libunistring5 set to manually installed. libquadmath0 is already the newest version (14.2.0-8). libquadmath0 set to manually installed. libuuid1 is already the newest version (2.40.2-11). perl is already the newest version (5.40.0-8). perl set to manually installed. cmake-data is already the newest version (3.31.1-1). cmake-data set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libaudit1 is already the newest version (1:4.0.2-2). base-passwd is already the newest version (3.6.5). debconf is already the newest version (1.5.87). libgnutls30t64 is already the newest version (3.8.8-2). libgnutls30t64 set to manually installed. mpi-default-dev is already the newest version (1.17). mpi-default-dev set to manually installed. libgomp1 is already the newest version (14.2.0-8). libgomp1 set to manually installed. gfortran-14-x86-64-linux-gnu is already the newest version (14.2.0-8). gfortran-14-x86-64-linux-gnu set to manually installed. cpp-14-x86-64-linux-gnu is already the newest version (14.2.0-8). cpp-14-x86-64-linux-gnu set to manually installed. python3-minimal is already the newest version (3.12.7-1). python3-minimal set to manually installed. autoconf is already the newest version (2.72-3). autoconf set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-8). libsasl2-modules-db set to manually installed. libxcb1 is already the newest version (1.17.0-2+b1). libxcb1 set to manually installed. binutils is already the newest version (2.43.50.20241126-3). binutils set to manually installed. libncursesw6 is already the newest version (6.5-2+b1). libncursesw6 set to manually installed. sysvinit-utils is already the newest version (3.11-1). libc-bin is already the newest version (2.40-4). debianutils is already the newest version (5.21). libgmp-dev is already the newest version (2:6.3.0+dfsg-2+b2). libgmp-dev set to manually installed. openmpi-bin is already the newest version (5.0.6-2). openmpi-bin set to manually installed. python3-inflect is already the newest version (7.3.1-2). python3-inflect set to manually installed. diffutils is already the newest version (1:3.10-1). libz3-4 is already the newest version (4.13.3-1). libz3-4 set to manually installed. make is already the newest version (4.3-4.1). make set to manually installed. libibverbs-dev is already the newest version (52.0-2+b1). libibverbs-dev set to manually installed. openssl is already the newest version (3.3.2-2). openssl set to manually installed. libibmad5 is already the newest version (52.0-2+b1). libibmad5 set to manually installed. passwd is already the newest version (1:4.16.0-5). passwd set to manually installed. libhwloc-plugins is already the newest version 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newest version (3.4.0-4). libeigen3-dev set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-2+b2). libgmpxx4ldbl set to manually installed. libnghttp2-14 is already the newest version (1.64.0-1). libnghttp2-14 set to manually installed. libarchive13t64 is already the newest version (3.7.4-1.1). libarchive13t64 set to manually installed. python3-packaging is already the newest version (24.2-1). python3-packaging set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libbrotli1 is already the newest version (1.1.0-2+b6). libbrotli1 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-6). libproc2-0 set to manually installed. binutils-common is already the newest version (2.43.50.20241126-3). binutils-common set to manually installed. python3-autocommand is already the newest version (2.2.2-3). python3-autocommand set to manually installed. libtinfo6 is already the newest version (6.5-2+b1). ncurses-bin is already the newest version (6.5-2+b1). python3-more-itertools is already the newest version (10.5.0-1). python3-more-itertools set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-2.1-7t64 set to manually installed. libcurl4t64 is already the newest version (8.11.0-1). libcurl4t64 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-7+b1). liblocale-gettext-perl set to manually installed. libsepol2 is already the newest version (3.7-1). libsepol2 set to manually installed. libedit2 is already the newest version (3.1-20240808-1). libedit2 set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. libpkgconf3 is already the newest version (1.8.1-4). libpkgconf3 set to manually installed. python3-urllib3 is already the newest version (2.0.7-2). python3-urllib3 set to manually installed. xz-utils is already the newest version (5.6.3-1+b1). xz-utils set to manually installed. coreutils is already the newest version (9.5-1+b1). libudev1 is already the newest version (257~rc2-3). libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libnl-3-dev is already the newest version (3.7.0-0.3+b1). libnl-3-dev set to manually installed. pkgconf is already the newest version (1.8.1-4). pkgconf set to manually installed. libuchardet0 is already the newest version (0.0.8-1+b2). libuchardet0 set to manually installed. libffi8 is already the newest version (3.4.6-1). libffi8 set to manually installed. libexpat1 is already the newest version (2.6.4-1). libexpat1 set to manually installed. python3-docutils is already the newest version (0.21.2+dfsg-2). python3-docutils set to manually installed. libubsan1 is already the newest version (14.2.0-8). libubsan1 set to manually installed. libuv1t64 is already the newest version (1.48.0-7). libuv1t64 set to manually installed. libstdc++6 is already the newest version (14.2.0-8). libstdc++6 set to manually installed. libsprng2 is already the newest version (2.0a-16). libsprng2 set to manually installed. libgssapi-krb5-2 is already the newest version (1.21.3-3). libgssapi-krb5-2 set to manually installed. ibverbs-providers is already the newest version (52.0-2+b1). ibverbs-providers set to manually installed. libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. libjsoncpp26 is already the newest version (1.9.6-3). libjsoncpp26 set to manually installed. gfortran-14 is already the newest version (14.2.0-8). gfortran-14 set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. libhwloc-dev is already the newest version (2.11.2-1). libhwloc-dev set to manually installed. liblzma5 is already the newest version (5.6.3-1+b1). automake is already the newest version (1:1.16.5-1.3). automake set to manually installed. libdrm-common is already the newest version (2.4.123-1). libdrm-common set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-1). libxdmcp6 set to manually installed. python3-requests is already the newest version (2.32.3+dfsg-1). python3-requests set to manually installed. python3-idna is already the newest version (3.8-2). python3-idna set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:14.2.0-1). gcc-x86-64-linux-gnu set to manually installed. perl-modules-5.40 is already the newest version (5.40.0-8). perl-modules-5.40 set to manually installed. libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:14.2.0-1). g++-x86-64-linux-gnu set to manually installed. dwz is already the newest version (0.15-1+b1). dwz set to manually installed. libgfortran5 is already the newest version (14.2.0-8). libgfortran5 set to manually installed. python3-chardet is already the newest version (5.2.0+dfsg-1). python3-chardet set to manually installed. libopenmpi-dev is already the newest version (5.0.6-2). libopenmpi-dev set to manually installed. libibumad3 is already the newest version (52.0-2+b1). libibumad3 set to manually installed. cmake is already the newest version (3.31.1-1). cmake set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. libpam-modules-bin is already the newest version (1.5.3-7+b1). groff-base is already the newest version (1.23.0-5). groff-base set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. libjs-sphinxdoc is already the newest version (7.4.7-4). libjs-sphinxdoc set to manually installed. libcom-err2 is already the newest version (1.47.1-1+b1). libcom-err2 set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1). libssh2-1t64 set to manually installed. The following NEW packages will be installed: pkg-config 127.0.0.1 - - [02/Mar/2026 10:06:09] "GET /./pkg-config_1.8.1-4_amd64.deb HTTP/1.1" 200 - 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 14.0 kB of archives. After this operation, 29.7 kB of additional disk space will be used. Get:1 http://localhost:41215 ./ pkg-config 1.8.1-4 [14.0 kB] Fetched 14.0 kB in 0s (0 B/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/ Selecting previously unselected package pkg-config:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 44311 files and directories currently installed.) Preparing to unpack .../pkg-config_1.8.1-4_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-4) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza/ Setting up pkg-config:amd64 (1.8.1-4) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza (Reading database ... 44316 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: PID 7158 exited with exit code 0 I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.mUcYxW6lza... I: success in 101.7271 seconds Downloading dependency 258 of 315: binutils-common:amd64=2.43.50.20241126-3 Downloading dependency 259 of 315: python3-autocommand:amd64=2.2.2-3 Downloading dependency 260 of 315: libtinfo6:amd64=6.5-2+b1 Downloading dependency 261 of 315: ncurses-bin:amd64=6.5-2+b1 Downloading dependency 262 of 315: python3-more-itertools:amd64=10.5.0-1 Downloading dependency 263 of 315: libevent-2.1-7t64:amd64=2.1.12-stable-10+b1 Downloading dependency 264 of 315: libcurl4t64:amd64=8.11.0-1 Downloading dependency 265 of 315: liblocale-gettext-perl:amd64=1.07-7+b1 Downloading dependency 266 of 315: libsepol2:amd64=3.7-1 Downloading dependency 267 of 315: libedit2:amd64=3.1-20240808-1 Downloading dependency 268 of 315: libgdbm6t64:amd64=1.24-2 Downloading dependency 269 of 315: libpkgconf3:amd64=1.8.1-4 Downloading dependency 270 of 315: python3-urllib3:amd64=2.0.7-2 Downloading dependency 271 of 315: xz-utils:amd64=5.6.3-1+b1 Downloading dependency 272 of 315: coreutils:amd64=9.5-1+b1 Downloading dependency 273 of 315: libudev1:amd64=257~rc2-3 Downloading dependency 274 of 315: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 275 of 315: libnl-3-dev:amd64=3.7.0-0.3+b1 Downloading dependency 276 of 315: pkgconf:amd64=1.8.1-4 Downloading dependency 277 of 315: libuchardet0:amd64=0.0.8-1+b2 Downloading dependency 278 of 315: libffi8:amd64=3.4.6-1 Downloading dependency 279 of 315: libexpat1:amd64=2.6.4-1 Downloading dependency 280 of 315: python3-docutils:amd64=0.21.2+dfsg-2 Downloading dependency 281 of 315: libubsan1:amd64=14.2.0-8 Downloading dependency 282 of 315: libuv1t64:amd64=1.48.0-7 Downloading dependency 283 of 315: libstdc++6:amd64=14.2.0-8 Downloading dependency 284 of 315: libsprng2:amd64=2.0a-16 Downloading dependency 285 of 315: libgssapi-krb5-2:amd64=1.21.3-3 Downloading dependency 286 of 315: ibverbs-providers:amd64=52.0-2+b1 Downloading dependency 287 of 315: libisl23:amd64=0.27-1 Downloading dependency 288 of 315: libjsoncpp26:amd64=1.9.6-3 Downloading dependency 289 of 315: gfortran-14:amd64=14.2.0-8 Downloading dependency 290 of 315: python3-jaraco.functools:amd64=4.1.0-1 Downloading dependency 291 of 315: libhwloc-dev:amd64=2.11.2-1 Downloading dependency 292 of 315: liblzma5:amd64=5.6.3-1+b1 Downloading dependency 293 of 315: automake:amd64=1:1.16.5-1.3 Downloading dependency 294 of 315: libdrm-common:amd64=2.4.123-1 Downloading dependency 295 of 315: libxdmcp6:amd64=1:1.1.5-1 Downloading dependency 296 of 315: python3-requests:amd64=2.32.3+dfsg-1 Downloading dependency 297 of 315: python3-idna:amd64=3.8-2 Downloading dependency 298 of 315: gcc-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 299 of 315: perl-modules-5.40:amd64=5.40.0-8 Downloading dependency 300 of 315: libmpc3:amd64=1.3.1-1+b3 Downloading dependency 301 of 315: g++-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 302 of 315: dwz:amd64=0.15-1+b1 Downloading dependency 303 of 315: libgfortran5:amd64=14.2.0-8 Downloading dependency 304 of 315: python3-chardet:amd64=5.2.0+dfsg-1 Downloading dependency 305 of 315: libopenmpi-dev:amd64=5.0.6-2 Downloading dependency 306 of 315: libibumad3:amd64=52.0-2+b1 Downloading dependency 307 of 315: cmake:amd64=3.31.1-1 Downloading dependency 308 of 315: libjansson4:amd64=2.14-2+b3 Downloading dependency 309 of 315: libpam-modules-bin:amd64=1.5.3-7+b1 Downloading dependency 310 of 315: groff-base:amd64=1.23.0-5 Downloading dependency 311 of 315: dh-autoreconf:amd64=20 Downloading dependency 312 of 315: libjs-sphinxdoc:amd64=7.4.7-4 Downloading dependency 313 of 315: libcom-err2:amd64=1.47.1-1+b1 Downloading dependency 314 of 315: bzip2:amd64=1.0.8-6 Downloading dependency 315 of 315: libssh2-1t64:amd64=1.11.1-1 env --chdir=/srv/rebuilderd/tmp/rebuilderd5aFT8T/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1732891901 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildXNRKgh/debrebuild.sbuildrc.zp7JWHtHr8bO sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --binNMU-changelog= iqtree (2.0.7+dfsg-1+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libopenmpi40. -- all / amd64 / i386 Build Daemon (x86-conova-01) Fri, 29 Nov 2024 14:51:41 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildXNRKgh/debrebuild.tar.610bxMuYlnxS --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --starting-build-commands=grep -iq "^Rules-Requires-Root:" "%p/debian/control" || sed -i "1iRules-Requires-Root: no" "%p/debian/control" --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=iqtree-2.0.7+dfsg /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl42-amd64.novalocal +==============================================================================+ | iqtree 2.0.7+dfsg-1+b2 (amd64) Mon, 02 Mar 2026 10:06:16 +0000 | +==============================================================================+ Package: iqtree Version: 2.0.7+dfsg-1+b2 Source Version: 2.0.7+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildXNRKgh/debrebuild.tar.610bxMuYlnxS to /srv/rebuilderd/tmp/tmp.sbuild.WsWlE3xHDO... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 02 Mar 2026 10:06:21 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1.dsc exists in /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 02 Mar 2026 10:06:22 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-LDxpgk/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 02 Mar 2026 10:06:25 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386) +------------------------------------------------------------------------------+ | Build environment Mon, 02 Mar 2026 10:06:25 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.73+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.73-1 (2026-02-17) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20241126-3 dpkg-dev_1.22.11 g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-4 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.10-1 Package versions: adduser_3.137 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.50.20241126-3 binutils-common_2.43.50.20241126-3 binutils-x86-64-linux-gnu_2.43.50.20241126-3 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 chrpath_0.18-1 cmake_3.31.1-1 cmake-data_3.31.1-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-x86-64-linux-gnu_14.2.0-8 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-x86-64-linux-gnu_14.2.0-8 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-8 gcc-14-base_14.2.0-8 gcc-14-x86-64-linux-gnu_14.2.0-8 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gfortran-14_14.2.0-8 gfortran-14-x86-64-linux-gnu_14.2.0-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 help2man_1.49.3 hostname_3.25 ibverbs-providers_52.0-2+b1 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2 libamdhip64-5_5.7.1-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-8 libatomic1_14.2.0-8 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2 libbinutils_2.43.50.20241126-3 libblkid1_2.40.2-11 libboost-dev_1.83.0.2+b2 libboost1.83-dev_1.83.0-3.2+b1 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-4 libc-dev-bin_2.40-4 libc6_2.40-4 libc6-dev_2.40-4 libcap-ng0_0.8.5-3+b1 libcap2_1:2.66-5+b1 libcbor0.10_0.10.2-2 libcc1-0_14.2.0-8 libcom-err2_1.47.1-1+b1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.50.20241126-3 libctf0_2.43.50.20241126-3 libcurl4t64_8.11.0-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.273 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libdrm-amdgpu1_2.4.123-1 libdrm-common_2.4.123-1 libdrm2_2.4.123-1 libedit2_3.1-20240808-1 libeigen3-dev_3.4.0-4 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libevent-core-2.1-7t64_2.1.12-stable-10+b1 libevent-dev_2.1.12-stable-10+b1 libevent-extra-2.1-7t64_2.1.12-stable-10+b1 libevent-openssl-2.1-7t64_2.1.12-stable-10+b1 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.6.4-1 libfabric1_1.17.0-3.1 libffi8_3.4.6-1 libfido2-1_1.15.0-1+b1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-14-dev_14.2.0-8 libgcc-s1_14.2.0-8 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.2.0-8 libgfortran5_14.2.0-8 libgmp-dev_2:6.3.0+dfsg-2+b2 libgmp10_2:6.3.0+dfsg-2+b2 libgmpxx4ldbl_2:6.3.0+dfsg-2+b2 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-8 libgprofng0_2.43.50.20241126-3 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1+b1 libhsa-runtime64-1_6.1.2-2 libhsakmt1_6.1.2+ds-1 libhwasan0_14.2.0-8 libhwloc-dev_2.11.2-1 libhwloc-plugins_2.11.2-1 libhwloc15_2.11.2-1 libibmad5_52.0-2+b1 libibumad3_52.0-2+b1 libibverbs-dev_52.0-2+b1 libibverbs1_52.0-2+b1 libicu72_72.1-5+b1 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-8 libjansson4_2.14-2+b3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_7.4.7-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-perl_4.10000-1 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libldap-2.5-0_2.5.18+dfsg-3+b1 libllvm17t64_1:17.0.6-18 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-8 libltdl-dev_2.4.7-8 libltdl7_2.4.7-8 liblz4-1_1.9.4-3+b1 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.2-11 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libmunge2_0.5.15-4+b1 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnl-3-200_3.7.0-0.3+b1 libnl-3-dev_3.7.0-0.3+b1 libnl-route-3-200_3.7.0-0.3+b1 libnl-route-3-dev_3.7.0-0.3+b1 libnsl2_1.3.0-3+b3 libnuma-dev_2.0.18-1+b1 libnuma1_2.0.18-1+b1 libopenmpi-dev_5.0.6-2 libopenmpi40_5.0.6-2 libp11-kit0_0.25.5-2+b1 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpciaccess0_0.17-3+b2 libpcre2-8-0_10.44-4 libperl5.40_5.40.0-8 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpmix-dev_5.0.4-1 libpmix2t64_5.0.4-1 libproc2-0_2:4.0.4-6 libpsl5t64_0.21.2-1.1+b1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2.1 libpython3-stdlib_3.12.7-1 libpython3.12-minimal_3.12.7-3 libpython3.12-stdlib_3.12.7-3 libquadmath0_14.2.0-8 librdmacm1t64_52.0-2+b1 libreadline8t64_8.2-5 librhash1_1.4.5-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20241126-3 libsmartcols1_2.40.2-11 libsprng2_2.0a-16 libsprng2-dev_2.0a-16 libsqlite3-0_3.46.1-1 libssh2-1t64_1.11.1-1 libssl3t64_3.3.2-2 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 libsystemd0_257~rc2-3 libtasn1-6_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3+b1 libtool_2.4.7-8 libtsan2_14.2.0-8 libubsan1_14.2.0-8 libuchardet0_0.0.8-1+b2 libucx0_1.17.0+ds-3 libudev1_257~rc2-3 libunistring5_1.2-1+b1 libuuid1_2.40.2-11 libuv1t64_1.48.0-7 libx11-6_2:1.8.10-2 libx11-data_2:1.8.10-2 libxau6_1:1.0.11-1 libxcb1_1.17.0-2+b1 libxdmcp6_1:1.1.5-1 libxext6_2:1.3.4-1+b2 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxnvctrl0_535.171.04-1+b1 libxxhash0_0.8.2-2+b2 libz3-4_4.13.3-1 libzstd1_1.5.6+dfsg-1+b1 linux-libc-dev_6.11.10-1 login.defs_1:4.16.0-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mpi-default-dev_1.17 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1+b2 openmpi-bin_5.0.6-2 openmpi-common_5.0.6-2 openssh-client_1:9.9p1-3 openssl_3.3.2-2 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-5 patch_2.7.6-7 perl_5.40.0-8 perl-base_5.40.0-8 perl-modules-5.40_5.40.0-8 pkg-config_1.8.1-4 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 python-babel-localedata_2.16.0-1 python3_3.12.7-1 python3-alabaster_0.7.16-0.1 python3-autocommand_2.2.2-3 python3-babel_2.16.0-1 python3-certifi_2024.8.30+dfsg-1 python3-chardet_5.2.0+dfsg-1 python3-charset-normalizer_3.4.0-1+b1 python3-defusedxml_0.7.1-2 python3-docutils_0.21.2+dfsg-2 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jinja2_3.1.3-1 python3-markupsafe_2.1.5-1+b2 python3-minimal_3.12.7-1 python3-more-itertools_10.5.0-1 python3-packaging_24.2-1 python3-pkg-resources_75.2.0-1 python3-pygments_2.18.0+dfsg-1 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.4.7-4 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3-urllib3_2.0.7-2 python3.12_3.12.7-3 python3.12-minimal_3.12.7-3 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_7.4.7-4 sysvinit-utils_3.11-1 tar_1.35+dfsg-3 time_1.9-0.2 tzdata_2024b-3 usr-is-merged_39 util-linux_2.40.2-11 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 02 Mar 2026 10:06:25 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree Binary: iqtree Architecture: amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 Version: 2.0.7+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Kevin Murray Homepage: http://www.cibiv.at/software/iqtree/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/iqtree Vcs-Git: https://salsa.debian.org/med-team/iqtree.git Testsuite: autopkgtest Testsuite-Triggers: time Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree deb science optional arch=amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386 Checksums-Sha1: 55d95bdac2da0ae814d1823a6e3fdd40cc41fe83 1581628 iqtree_2.0.7+dfsg.orig.tar.xz f80d1bef58520f5fc6bafa50347d04056671a579 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz Checksums-Sha256: 95a3a9c3b32aeb8caa63307808fed7fad68f20f877f3fe5fe751af1d49cbdb86 1581628 iqtree_2.0.7+dfsg.orig.tar.xz 704055ba4585527dacedf6b6cdf5d796c4fd20828fcd48c4d6856601b422e9d6 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz Files: 1c1bbda0de4ede3114cd8f7c67128cac 1581628 iqtree_2.0.7+dfsg.orig.tar.xz c48f5516b5986759881c990fffc68664 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHqvkgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFovg//f8yUsqV1QtBVBwfvLfRrwYw7EjlAL9Qh /9bikhd+WiWlMPdFL2/pUJT0t3bvDugGGECPrBNlTx9pfcpDNCiO0UHi9kJ8CO3F LcJwsusN5MOuVmIozXExklVg2HvXuwNjy/DSiIjSlcDrsldel4PITa6zDedX+GyQ XZ8f2hQnQnGhpY0M/jBGPDWDQp+87xU0kxy8jxDQi0c9+9c254KZaMK8IqOgxkzJ xkVzUW1as784fAnhTVH5Th40GOHygtFgFD0ttVxs1W1xHFL/yhR9NEs9bZU0rtew Sv/quf+8zMqX+hkGqirGjlB+emtxuHBowmwxmEIwP1BUvy9saszNBV5uEgpGEYrZ PwqY4MyqCmYmY55FRansqHeZ7s4x6X9bjPwwWfhXjvC1U+8bvToheHDpNp6RK3iX NKtDhptlp7oOHs0rzYsVScYLQrGQU0vMveFZvD4FUhGG693eN8Ed3dLYHCvSwVnH IXuwt+c7RuRRAHo4F1V3ONOcmfrPDrfhsG64FkYNDBXh5opKntFdRSWgjOWgQStS jyBHT305IVT1E5pZAywKb1jwVUw44RalMKHZdm3zRhkBynye3D+7+OFSTg4mr2Qk FKiZsa1mHLU3WQ6L2PYyO12NJwfrnCHKYdmgSkn32K/ojvo3csiU+JVl8q9CEKEs atE/Jqjs97c= =Pwr1 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./iqtree_2.0.7+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting iqtree in /build/reproducible-path/iqtree-2.0.7+dfsg dpkg-source: info: unpacking iqtree_2.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz Install fakeroot ---------------- Setup apt archive ----------------- Merged Build-Depends: fakeroot Filtered Build-Depends: fakeroot dpkg-deb: building package 'sbuild-build-depends-fakeroot-dummy' in '/build/reproducible-path/resolver-LDxpgk/apt_archive/sbuild-build-depends-fakeroot-dummy.deb'. Install fakeroot build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 2.0.7+dfsg-1+b2 +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 02 Mar 2026 10:06:29 +0000 | +------------------------------------------------------------------------------+ grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/control" ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- I: Finished running 'grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/control"'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1732891901 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1+b2 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:74 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- clang-tidy not found. -- Configuring done (1.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:74 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- clang-tidy not found. -- Configuring done (1.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:74 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- clang-tidy not found. -- Configuring done (2.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 4%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function ‘virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)’: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c [ 5%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 6%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 7%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c [ 19%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c [ 19%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 22%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 22%] Built target pll [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 27%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 27%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 27%] Built target ncl make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 28%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 29%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 31%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 31%] Built target lbfgsb [ 31%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 32%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 32%] Built target gsl [ 32%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c [ 32%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c [ 32%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c [ 33%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c [ 34%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 35%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 35%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 35%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 36%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 36%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 36%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 36%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 [ 37%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 37%] Built target terraphast make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 37%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c [ 37%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 38%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 38%] Built target booster [ 39%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 39%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 39%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c [ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 42%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 42%] Built target pllavx make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp [ 43%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 45%] Built target whtest [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 45%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 46%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 47%] Built target nclextra make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 47%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 49%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 50%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 50%] Built target kernelsse make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 50%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 55%] Built target kernelavx [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 57%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 57%] Built target kernelfma [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 59%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 65%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 66%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 66%] Built target utils In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ [ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 68%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 69%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 70%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 71%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 72%] Linking CXX static library libyaml-cpp.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake [ 72%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 72%] Built target yaml-cpp [ 72%] Built target pda make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 72%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 [ 75%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 75%] Built target phyloYAML make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 75%] Built target alignment [ 76%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 77%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp [ 78%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 81%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 85%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 85%] Built target main [ 85%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file,CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp [ 0%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 3%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 5%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function ‘virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)’: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 6%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 7%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/queue.c.o [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 16%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c [ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c [ 19%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 22%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 22%] Built target pll make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 22%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 25%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c [ 26%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 26%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 28%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 28%] Built target lbfgsb make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 29%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 29%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 31%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 31%] Built target gsl make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 32%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 32%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c [ 32%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 32%] Built target terraphast make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 33%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 33%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c [ 34%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c [ 34%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c [ 34%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 34%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 35%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 35%] Built target ncl [ 36%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 36%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 36%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c [ 37%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c [ 37%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 39%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 39%] Built target booster [ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 39%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 39%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 40%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 [ 41%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 41%] Built target nclextra make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 43%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c [ 44%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 45%] Built target pllavx [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 45%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 45%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 46%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 46%] Built target whtest make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 46%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 47%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [ 48%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 50%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 50%] Built target kernelsse make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 50%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 50%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp [ 51%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 51%] Built target kernelfma [ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp [ 56%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 56%] Built target kernelavx [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 60%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 60%] Built target utils [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 60%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 67%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 67%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 69%] Linking CXX static library libyaml-cpp.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 69%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 69%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 70%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp [ 72%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 72%] Built target phyloYAML [ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp [ 74%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake [ 74%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 74%] Built target pda [ 75%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 75%] Built target alignment make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 76%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 81%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 82%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 86%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 86%] Built target main [ 87%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file,CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 3%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 4%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function ‘virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)’: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ [ 5%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c [ 5%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 6%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 7%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c [ 19%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c [ 19%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 22%] Built target pll make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 22%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 23%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 23%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 24%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 24%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c [ 25%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 25%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 25%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 27%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 27%] Built target lbfgsb [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 28%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake [ 29%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 29%] Built target ncl make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" [ 29%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 30%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 31%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 31%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 33%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c [ 33%] Linking CXX static library libgsl.a [ 33%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 33%] Built target gsl make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 34%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 34%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 34%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 34%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o 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'/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 34%] Built target terraphast make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 35%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 36%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 37%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 37%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 38%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 38%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c [ 39%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c [ 40%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 41%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 41%] Built target booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 41%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 41%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 43%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 43%] Built target whtest make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 44%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 45%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 45%] Built target pllavx [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 47%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp [ 48%] Built target nclextra make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 48%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 48%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 49%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 49%] Built target kernelsse [ 49%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 52%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 53%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp [ 55%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Built target kernelfma [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 58%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 58%] Built target kernelavx [ 58%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 62%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 63%] Built target utils [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 68%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 68%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 69%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 69%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp [ 70%] Linking CXX static library libyaml-cpp.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 70%] Built target yaml-cpp [ 70%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 71%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 72%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp [ 72%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 74%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 74%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 74%] Built target pda [ 75%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 75%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 [ 76%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 76%] Built target phyloYAML [ 76%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 76%] Built target alignment make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 77%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 84%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 85%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 85%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 85%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 86%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 86%] Built target main [ 87%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file,CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ... + time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Nov 29 2024 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy Seed: 829293 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Mon Mar 2 10:13:53 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.003 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11239.861 Optimal log-likelihood: -11239.650 Rate parameters: A-C: 1.45141 A-G: 2.32125 A-T: 1.74102 C-G: 1.90808 C-T: 2.78665 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.550 Parameters optimization took 1 rounds (0.020 sec) Time for fast ML tree search: 0.194 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11797.808 93 23781.615 23841.905 24149.025 2 GTR+F+I 11556.535 94 23301.070 23362.869 23672.430 3 GTR+F+G4 11255.917 94 22699.833 22761.633 23071.194 4 GTR+F+I+G4 11239.658 95 22669.316 22732.649 23044.627 5 GTR+F+R2 11346.095 95 22882.189 22945.522 23257.500 6 GTR+F+R3 11241.184 97 22676.368 22742.843 23059.580 7 GTR+F+R4 11233.752 99 22665.504 22735.223 23056.618 8 GTR+F+R5 11233.332 101 22668.665 22741.728 23067.680 17 SYM+I+G4 11242.729 92 22669.457 22728.261 23032.916 30 TVM+F+I+G4 11242.143 94 22672.286 22734.085 23043.646 43 TVMe+I+G4 11244.615 91 22671.230 22728.573 23030.739 56 TIM3+F+I+G4 11253.755 93 22693.511 22753.800 23060.920 69 TIM3e+I+G4 11257.581 90 22695.161 22751.066 23050.719 82 TIM2+F+I+G4 11257.451 93 22700.903 22761.192 23068.312 95 TIM2e+I+G4 11265.345 90 22710.689 22766.594 23066.247 108 TIM+F+I+G4 11245.392 93 22676.783 22737.073 23044.193 121 TIMe+I+G4 11252.268 90 22684.536 22740.441 23040.094 134 TPM3u+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 147 TPM3+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 160 TPM2u+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 173 TPM2+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 186 K3Pu+F+I+G4 11247.847 92 22679.694 22738.498 23043.153 199 K3P+I+G4 11254.005 89 22686.010 22740.500 23037.617 212 TN+F+I+G4 11257.649 92 22699.298 22758.102 23062.757 225 TNe+I+G4 11265.431 89 22708.861 22763.351 23060.468 238 HKY+F+I+G4 11260.239 91 22702.477 22759.820 23061.986 251 K2P+I+G4 11267.270 88 22710.539 22763.638 23058.196 264 F81+F+I+G4 11308.833 90 22797.666 22853.571 23153.224 277 JC+I+G4 11313.164 87 22800.329 22852.059 23144.035 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 1.971 seconds (0h:0m:1s) Wall-clock time for ModelFinder: 1.992 seconds (0h:0m:1s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.590 / Estimate: 0.000, 0.970 / LogL: -11259.840 Init pinv, alpha: 0.012, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.628 Init pinv, alpha: 0.023, 1.590 / Estimate: 0.084, 1.581 / LogL: -11244.611 Init pinv, alpha: 0.035, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.613 Init pinv, alpha: 0.046, 1.590 / Estimate: 0.084, 1.582 / LogL: -11244.612 Init pinv, alpha: 0.058, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.618 Init pinv, alpha: 0.069, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.620 Init pinv, alpha: 0.081, 1.590 / Estimate: 0.084, 1.580 / LogL: -11244.615 Init pinv, alpha: 0.093, 1.590 / Estimate: 0.085, 1.592 / LogL: -11244.613 Init pinv, alpha: 0.104, 1.590 / Estimate: 0.086, 1.598 / LogL: -11244.621 Optimal pinv,alpha: 0.084, 1.581 / LogL: -11244.611 Parameters optimization took 0.682 sec Computing ML distances based on estimated model parameters... 0.024 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -11270.724 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.342 second Computing log-likelihood of 98 initial trees ... 0.415 seconds Current best score: -11244.611 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11244.583 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.129 Iteration 10 / LogL: -11231.920 / Time: 0h:0m:2s Iteration 20 / LogL: -11231.302 / Time: 0h:0m:2s Finish initializing candidate tree set (14) Current best tree score: -11225.129 / CPU time: 2.074 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11227.820 / Time: 0h:0m:3s (0h:0m:9s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 31: -11224.961 Iteration 40 / LogL: -11225.610 / Time: 0h:0m:4s (0h:0m:10s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 47: -11224.868 Iteration 50 / LogL: -11255.900 / Time: 0h:0m:5s (0h:0m:11s left) Iteration 60 / LogL: -11224.995 / Time: 0h:0m:6s (0h:0m:9s left) Iteration 70 / LogL: -11225.138 / Time: 0h:0m:7s (0h:0m:8s left) Iteration 80 / LogL: -11225.575 / Time: 0h:0m:8s (0h:0m:6s left) Iteration 90 / LogL: -11224.980 / Time: 0h:0m:9s (0h:0m:5s left) Iteration 100 / LogL: -11226.126 / Time: 0h:0m:9s (0h:0m:4s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 101: -11224.070 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 108: -11223.053 Iteration 110 / LogL: -11240.444 / Time: 0h:0m:10s (0h:0m:9s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 117: -11222.782 Iteration 120 / LogL: -11222.793 / Time: 0h:0m:11s (0h:0m:9s left) Iteration 130 / LogL: -11222.912 / Time: 0h:0m:12s (0h:0m:8s left) Iteration 140 / LogL: -11223.011 / Time: 0h:0m:13s (0h:0m:7s left) Iteration 150 / LogL: -11223.879 / Time: 0h:0m:14s (0h:0m:6s left) Iteration 160 / LogL: -11222.795 / Time: 0h:0m:14s (0h:0m:5s left) Iteration 170 / LogL: -11224.646 / Time: 0h:0m:15s (0h:0m:4s left) Iteration 180 / LogL: -11222.825 / Time: 0h:0m:16s (0h:0m:3s left) Iteration 190 / LogL: -11223.088 / Time: 0h:0m:17s (0h:0m:2s left) UPDATE BEST LOG-LIKELIHOOD: -11222.782 Iteration 200 / LogL: -11224.175 / Time: 0h:0m:18s (0h:0m:1s left) Iteration 210 / LogL: -11222.947 / Time: 0h:0m:19s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 218 ITERATIONS / Time: 0h:0m:19s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.782 Optimal log-likelihood: -11222.778 Rate parameters: A-C: 1.53695 A-G: 2.64127 A-T: 1.69623 C-G: 2.00514 C-T: 2.64127 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.083 Gamma shape alpha: 1.529 Parameters optimization took 1 rounds (0.017 sec) BEST SCORE FOUND : -11222.778 Total tree length: 12.603 Total number of iterations: 218 CPU time used for tree search: 18.742 sec (0h:0m:18s) Wall-clock time used for tree search: 19.120 sec (0h:0m:19s) Total CPU time used: 19.493 sec (0h:0m:19s) Total wall-clock time used: 19.873 sec (0h:0m:19s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Mon Mar 2 10:14:15 2026 21.46user 0.37system 0:21.87elapsed 99%CPU (0avgtext+0avgdata 15432maxresident)k 0inputs+224outputs (0major+2150minor)pagefaults 0swaps + time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.0.7 for Linux 64-bit built Nov 29 2024 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo Seed: 703169 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Mon Mar 2 10:14:15 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.003 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11221.199 Optimal log-likelihood: -11221.077 Rate parameters: A-C: 1.43742 A-G: 2.31924 A-T: 1.70852 C-G: 1.87193 C-T: 2.80680 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.499 Parameters optimization took 1 rounds (0.018 sec) Time for fast ML tree search: 0.191 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11789.714 93 23765.428 23825.718 24132.838 2 GTR+F+I 11547.061 94 23282.121 23343.920 23653.482 3 GTR+F+G4 11235.601 94 22659.201 22721.001 23030.562 4 GTR+F+I+G4 11221.091 95 22632.183 22695.516 23007.494 5 GTR+F+R2 11334.887 95 22859.775 22923.108 23235.086 6 GTR+F+R3 11221.215 97 22636.430 22702.905 23019.642 7 GTR+F+R4 11214.782 99 22627.564 22697.282 23018.677 8 GTR+F+R5 11214.792 101 22631.585 22704.649 23030.600 17 SYM+I+G4 11224.580 92 22633.161 22691.965 22996.620 30 TVM+F+I+G4 11223.880 94 22635.761 22697.560 23007.121 43 TVMe+I+G4 11226.717 91 22635.434 22692.777 22994.943 56 TIM3+F+I+G4 11234.231 93 22654.462 22714.752 23021.872 69 TIM3e+I+G4 11238.334 90 22656.667 22712.572 23012.225 82 TIM2+F+I+G4 11237.946 93 22661.893 22722.182 23029.302 95 TIM2e+I+G4 11246.029 90 22672.057 22727.962 23027.615 108 TIM+F+I+G4 11226.693 93 22639.387 22699.677 23006.797 121 TIMe+I+G4 11233.948 90 22647.897 22703.801 23003.454 134 TPM3u+F+I+G4 11237.187 92 22658.374 22717.178 23021.833 147 TPM3+F+I+G4 11237.187 92 22658.374 22717.178 23021.833 160 TPM2u+F+I+G4 11240.787 92 22665.575 22724.379 23029.034 173 TPM2+F+I+G4 11240.787 92 22665.575 22724.379 23029.034 186 K3Pu+F+I+G4 11229.447 92 22642.894 22701.698 23006.353 199 K3P+I+G4 11235.913 89 22649.826 22704.315 23001.433 212 TN+F+I+G4 11238.125 92 22660.249 22719.054 23023.709 225 TNe+I+G4 11246.111 89 22670.222 22724.712 23021.830 238 HKY+F+I+G4 11240.990 91 22663.980 22721.322 23023.488 251 K2P+I+G4 11248.162 88 22672.323 22725.421 23019.980 264 F81+F+I+G4 11292.699 90 22765.397 22821.302 23120.955 277 JC+I+G4 11297.068 87 22768.135 22819.865 23111.841 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 1.859 seconds (0h:0m:1s) Wall-clock time for ModelFinder: 1.889 seconds (0h:0m:1s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.544 / Estimate: 0.000, 0.944 / LogL: -11240.361 Init pinv, alpha: 0.012, 1.544 / Estimate: 0.083, 1.533 / LogL: -11226.719 Init pinv, alpha: 0.023, 1.544 / Estimate: 0.083, 1.531 / LogL: -11226.721 Init pinv, alpha: 0.035, 1.544 / Estimate: 0.083, 1.530 / LogL: -11226.722 Init pinv, alpha: 0.046, 1.544 / Estimate: 0.083, 1.534 / LogL: -11226.719 Init pinv, alpha: 0.058, 1.544 / Estimate: 0.083, 1.530 / LogL: -11226.723 Init pinv, alpha: 0.069, 1.544 / Estimate: 0.082, 1.528 / LogL: -11226.724 Init pinv, alpha: 0.081, 1.544 / Estimate: 0.083, 1.535 / LogL: -11226.717 Init pinv, alpha: 0.093, 1.544 / Estimate: 0.084, 1.548 / LogL: -11226.718 Init pinv, alpha: 0.104, 1.544 / Estimate: 0.085, 1.554 / LogL: -11226.725 Optimal pinv,alpha: 0.083, 1.535 / LogL: -11226.717 Parameters optimization took 0.757 sec Computing ML distances based on estimated model parameters... 0.023 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -11271.085 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.340 second Computing log-likelihood of 98 initial trees ... 0.419 seconds Current best score: -11226.717 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.745 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.131 Iteration 10 / LogL: -11231.206 / Time: 0h:0m:2s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 17: -11223.029 Iteration 20 / LogL: -11231.494 / Time: 0h:0m:2s Finish initializing candidate tree set (17) Current best tree score: -11223.029 / CPU time: 2.130 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 24: -11222.774 Iteration 30 / LogL: -11223.010 / Time: 0h:0m:3s (0h:0m:12s left) Iteration 40 / LogL: -11225.738 / Time: 0h:0m:4s (0h:0m:10s left) Iteration 50 / LogL: -11222.784 / Time: 0h:0m:5s (0h:0m:8s left) Iteration 60 / LogL: -11224.427 / Time: 0h:0m:6s (0h:0m:7s left) Iteration 70 / LogL: -11222.841 / Time: 0h:0m:7s (0h:0m:5s left) Iteration 80 / LogL: -11223.416 / Time: 0h:0m:8s (0h:0m:4s left) Iteration 90 / LogL: -11223.313 / Time: 0h:0m:9s (0h:0m:3s left) Iteration 100 / LogL: -11222.814 / Time: 0h:0m:9s (0h:0m:2s left) Iteration 110 / LogL: -11222.780 / Time: 0h:0m:10s (0h:0m:1s left) Iteration 120 / LogL: -11222.977 / Time: 0h:0m:11s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -11222.773 TREE SEARCH COMPLETED AFTER 125 ITERATIONS / Time: 0h:0m:12s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.773 Optimal log-likelihood: -11222.772 Rate parameters: A-C: 1.51658 A-G: 2.61031 A-T: 1.67317 C-G: 1.98209 C-T: 2.61031 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.530 Parameters optimization took 1 rounds (0.019 sec) BEST SCORE FOUND : -11222.772 Total tree length: 12.601 Total number of iterations: 125 CPU time used for tree search: 11.072 sec (0h:0m:11s) Wall-clock time used for tree search: 11.301 sec (0h:0m:11s) Total CPU time used: 11.897 sec (0h:0m:11s) Total wall-clock time used: 12.131 sec (0h:0m:12s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Mon Mar 2 10:14:29 2026 13.76user 0.23system 0:14.02elapsed 99%CPU (0avgtext+0avgdata 14892maxresident)k 0inputs+200outputs (0major+4465minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.cyuvjq 35.23user 0.63system 0:35.93elapsed 99%CPU (0avgtext+0avgdata 15432maxresident)k 0inputs+472outputs (0major+8246minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j6 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j6 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_install find debian -name iqtree2-mpi -exec chrpath --delete \{\} \; find debian -name iqtree2-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' mkdir -p /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="2.0.7+dfsg" /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb'. dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1+b2_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree_2.0.7+dfsg-1+b2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-03-02T10:15:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 02 Mar 2026 10:15:51 +0000 | +------------------------------------------------------------------------------+ iqtree_2.0.7+dfsg-1+b2_amd64.changes: ------------------------------------- Format: 1.8 Date: Fri, 29 Nov 2024 14:51:41 +0000 Source: iqtree (2.0.7+dfsg-1) Binary: iqtree iqtree-dbgsym Binary-Only: yes Architecture: amd64 Version: 2.0.7+dfsg-1+b2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: all / amd64 / i386 Build Daemon (x86-conova-01) Description: iqtree - efficient phylogenetic software by maximum likelihood Changes: iqtree (2.0.7+dfsg-1+b2) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libopenmpi40. Checksums-Sha1: b16df14525c10789351cb73c386ded05e39f1258 87050812 iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb 3ebe76b5b7cb4c4d6062762a56e622f05ca929a2 10612 iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo 82671c475ad457209fa8509d2f330ef1ef93c7ef 3653860 iqtree_2.0.7+dfsg-1+b2_amd64.deb Checksums-Sha256: 035485f98371f29e58f1f92c791b44a97b3d00e810fea0b5531f3e503a9e45da 87050812 iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb d23f10b8b9431b6ab8d45d790c42b60a7625c0a41035dfc65e6010f5cb5f282b 10612 iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo bb0a21cd3b8a4d8cdccc031024f42023883fd7c56893fd260cdc6904e20c5347 3653860 iqtree_2.0.7+dfsg-1+b2_amd64.deb Files: 067d632009e1d5d109427c9649e79fd3 87050812 debug optional iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb 4d29905d63fcd7ade8e1cdffc4ae0b1e 10612 science optional iqtree_2.0.7+dfsg-1+b2_amd64.buildinfo 6d6f74236acd1db3e2be567cdce88a7a 3653860 science optional iqtree_2.0.7+dfsg-1+b2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 02 Mar 2026 10:15:52 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree (2.0.7+dfsg-1) Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.0.7+dfsg-1+b2 Binary-Only-Changes: iqtree (2.0.7+dfsg-1+b2) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libopenmpi40. . -- all / amd64 / i386 Build Daemon (x86-conova-01) Fri, 29 Nov 2024 14:51:41 +0000 Checksums-Md5: 067d632009e1d5d109427c9649e79fd3 87050812 iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb 6d6f74236acd1db3e2be567cdce88a7a 3653860 iqtree_2.0.7+dfsg-1+b2_amd64.deb Checksums-Sha1: b16df14525c10789351cb73c386ded05e39f1258 87050812 iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb 82671c475ad457209fa8509d2f330ef1ef93c7ef 3653860 iqtree_2.0.7+dfsg-1+b2_amd64.deb Checksums-Sha256: 035485f98371f29e58f1f92c791b44a97b3d00e810fea0b5531f3e503a9e45da 87050812 iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb bb0a21cd3b8a4d8cdccc031024f42023883fd7c56893fd260cdc6904e20c5347 3653860 iqtree_2.0.7+dfsg-1+b2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 02 Mar 2026 10:15:49 +0000 Build-Path: /build/reproducible-path/iqtree-2.0.7+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: adduser (= 3.137), autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.5), bash (= 5.2.32-1+b2), binutils (= 2.43.50.20241126-3), binutils-common (= 2.43.50.20241126-3), binutils-x86-64-linux-gnu (= 2.43.50.20241126-3), bsdextrautils (= 2.40.2-11), bsdutils (= 1:2.40.2-11), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20240203), chrpath (= 0.18-1), cmake (= 3.31.1-1), cmake-data (= 3.31.1-1), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-8), cpp-14-x86-64-linux-gnu (= 14.2.0-8), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-9), debconf (= 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libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnl-3-200 (= 3.7.0-0.3+b1), libnl-3-dev (= 3.7.0-0.3+b1), libnl-route-3-200 (= 3.7.0-0.3+b1), libnl-route-3-dev (= 3.7.0-0.3+b1), libnsl2 (= 1.3.0-3+b3), libnuma-dev (= 2.0.18-1+b1), libnuma1 (= 2.0.18-1+b1), libopenmpi-dev (= 5.0.6-2), libopenmpi40 (= 5.0.6-2), libp11-kit0 (= 0.25.5-2+b1), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpciaccess0 (= 0.17-3+b2), libpcre2-8-0 (= 10.44-4), libperl5.40 (= 5.40.0-8), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpmix-dev (= 5.0.4-1), libpmix2t64 (= 5.0.4-1), libproc2-0 (= 2:4.0.4-6), libpsl5t64 (= 0.21.2-1.1+b1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2.1), libpython3-stdlib (= 3.12.7-1), libpython3.12-minimal (= 3.12.7-3), libpython3.12-stdlib (= 3.12.7-3), libquadmath0 (= 14.2.0-8), librdmacm1t64 (= 52.0-2+b1), libreadline8t64 (= 8.2-5), librhash1 (= 1.4.5-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsemanage-common (= 3.7-2), libsemanage2 (= 3.7-2+b1), libsepol2 (= 3.7-1), libsframe1 (= 2.43.50.20241126-3), libsmartcols1 (= 2.40.2-11), libsprng2 (= 2.0a-16), libsprng2-dev (= 2.0a-16), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.3.2-2), libstdc++-14-dev (= 14.2.0-8), libstdc++6 (= 14.2.0-8), libsystemd0 (= 257~rc2-3), libtasn1-6 (= 4.19.0-3+b3), libtinfo6 (= 6.5-2+b1), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3+b1), libtool (= 2.4.7-8), libtsan2 (= 14.2.0-8), libubsan1 (= 14.2.0-8), libuchardet0 (= 0.0.8-1+b2), libucx0 (= 1.17.0+ds-3), libudev1 (= 257~rc2-3), libunistring5 (= 1.2-1+b1), libuuid1 (= 2.40.2-11), libuv1t64 (= 1.48.0-7), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b2), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxnvctrl0 (= 535.171.04-1+b1), libxxhash0 (= 0.8.2-2+b2), libz3-4 (= 4.13.3-1), libzstd1 (= 1.5.6+dfsg-1+b1), linux-libc-dev (= 6.11.10-1), login.defs (= 1:4.16.0-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mpi-default-dev (= 1.17), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1+b2), openmpi-bin (= 5.0.6-2), openmpi-common (= 5.0.6-2), openssh-client (= 1:9.9p1-3), openssl (= 3.3.2-2), openssl-provider-legacy (= 3.3.2-2), passwd (= 1:4.16.0-5), patch (= 2.7.6-7), perl (= 5.40.0-8), perl-base (= 5.40.0-8), perl-modules-5.40 (= 5.40.0-8), pkg-config (= 1.8.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), python-babel-localedata (= 2.16.0-1), python3 (= 3.12.7-1), python3-alabaster (= 0.7.16-0.1), python3-autocommand (= 2.2.2-3), python3-babel (= 2.16.0-1), python3-certifi (= 2024.8.30+dfsg-1), python3-chardet (= 5.2.0+dfsg-1), python3-charset-normalizer (= 3.4.0-1+b1), python3-defusedxml (= 0.7.1-2), python3-docutils (= 0.21.2+dfsg-2), python3-idna (= 3.8-2), python3-imagesize (= 1.4.1-1), python3-inflect (= 7.3.1-2), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.1.0-1), python3-jinja2 (= 3.1.3-1), python3-markupsafe (= 2.1.5-1+b2), python3-minimal (= 3.12.7-1), python3-more-itertools (= 10.5.0-1), python3-packaging (= 24.2-1), python3-pkg-resources (= 75.2.0-1), python3-pygments (= 2.18.0+dfsg-1), python3-requests (= 2.32.3+dfsg-1), python3-roman (= 4.2-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 7.4.7-4), python3-typeguard (= 4.4.1-1), python3-typing-extensions (= 4.12.2-2), python3-urllib3 (= 2.0.7-2), python3.12 (= 3.12.7-3), python3.12-minimal (= 3.12.7-3), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 7.4.7-4), sysvinit-utils (= 3.11-1), tar (= 1.35+dfsg-3), time (= 1.9-0.2), tzdata (= 2024b-3), usr-is-merged (= 39), util-linux (= 2.40.2-11), xml-core (= 0.19), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1732891901" +------------------------------------------------------------------------------+ | Package contents Mon, 02 Mar 2026 10:15:52 +0000 | +------------------------------------------------------------------------------+ iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb --------------------------------------- new Debian package, version 2.0. size 87050812 bytes: control archive=704 bytes. 481 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: iqtree-dbgsym Source: iqtree (2.0.7+dfsg-1) Version: 2.0.7+dfsg-1+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 91312 Depends: iqtree (= 2.0.7+dfsg-1+b2) Section: debug Priority: optional Description: debug symbols for iqtree Build-Ids: 8628dc5cf7744c750f74cdd80bea874646c0bc32 93e18b05a929c54ff17e7423e23b352e829f849e fb0df4561826e84ea160d2a9ba1a294d724e350f drwxr-xr-x root/root 0 2024-11-29 14:51 ./ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.build-id/86/ -rw-r--r-- root/root 26653032 2024-11-29 14:51 ./usr/lib/debug/.build-id/86/28dc5cf7744c750f74cdd80bea874646c0bc32.debug drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.build-id/93/ -rw-r--r-- root/root 26732616 2024-11-29 14:51 ./usr/lib/debug/.build-id/93/e18b05a929c54ff17e7423e23b352e829f849e.debug drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.build-id/fb/ -rw-r--r-- root/root 26652856 2024-11-29 14:51 ./usr/lib/debug/.build-id/fb/0df4561826e84ea160d2a9ba1a294d724e350f.debug drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 13447232 2024-11-29 14:51 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree.debug drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-11-29 14:51 ./usr/share/doc/iqtree-dbgsym -> iqtree iqtree_2.0.7+dfsg-1+b2_amd64.deb -------------------------------- new Debian package, version 2.0. size 3653860 bytes: control archive=1516 bytes. 1455 bytes, 30 lines control 1023 bytes, 15 lines md5sums Package: iqtree Source: iqtree (2.0.7+dfsg-1) Version: 2.0.7+dfsg-1+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 25632 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 14), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://www.cibiv.at/software/iqtree/ Description: efficient phylogenetic software by maximum likelihood IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others: . * A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015) * An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013). * A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments. * Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest. * Finding best partition scheme like PartitionFinder. * Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes. * Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014) drwxr-xr-x root/root 0 2024-11-29 14:51 ./ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/bin/ -rwxr-xr-x root/root 7930976 2024-11-29 14:51 ./usr/bin/iqtree2 -rwxr-xr-x root/root 7947360 2024-11-29 14:51 ./usr/bin/iqtree2-mpi -rwxr-xr-x root/root 7930976 2024-11-29 14:51 ./usr/bin/iqtree2-omp drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/doc/iqtree/ -rw-r--r-- root/root 278 2022-01-21 11:05 ./usr/share/doc/iqtree/README.test -rw-r--r-- root/root 236 2024-11-29 14:51 ./usr/share/doc/iqtree/changelog.Debian.amd64.gz -rw-r--r-- root/root 587 2024-11-29 14:51 ./usr/share/doc/iqtree/changelog.Debian.gz -rw-r--r-- root/root 7971 2022-01-21 11:05 ./usr/share/doc/iqtree/copyright drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/doc/iqtree/examples/ -rw-r--r-- root/root 2237314 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.cf -rw-r--r-- root/root 174 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.nex -rw-r--r-- root/root 34178 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.phy -rw-r--r-- root/root 121669 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/models.nex -rw-r--r-- root/root 2188 2022-01-21 11:05 ./usr/share/doc/iqtree/run-unit-test drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-29 14:51 ./usr/share/man/man1/ -rw-r--r-- root/root 5095 2024-11-29 14:51 ./usr/share/man/man1/iqtree2-mpi.1.gz -rw-r--r-- root/root 5093 2024-11-29 14:51 ./usr/share/man/man1/iqtree2-omp.1.gz -rw-r--r-- root/root 5072 2024-11-29 14:51 ./usr/share/man/man1/iqtree2.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 02 Mar 2026 10:15:53 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 02 Mar 2026 10:15:53 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 02 Mar 2026 10:15:55 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 2652172 Build-Time: 562 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderd5aFT8T/inputs/iqtree_2.0.7+dfsg-1.dsc Machine Architecture: amd64 Package: iqtree Package-Time: 575 Source-Version: 2.0.7+dfsg-1 Space: 2652172 Status: successful Version: 2.0.7+dfsg-1+b2 -------------------------------------------------------------------------------- Finished at 2026-03-02T10:15:51Z Build needed 00:09:35, 2652172k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderd5aFT8T/out checking iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb: size differs for iqtree-dbgsym_2.0.7+dfsg-1+b2_amd64.deb