=============================================================================== 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/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo Source: iqtree Version: 2.4.0+dfsg-2 rebuilderd-worker node: osuosl42-amd64 +------------------------------------------------------------------------------+ | Downloading sources Tue, 21 Jul 2026 10:58:54 +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 [151 kB] Get:7 https://deb.debian.org/debian sid InRelease [193 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [185 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 [1,840 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [89.5 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [276 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3,376 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [7,856 B] Get:18 https://deb.debian.org/debian forky/main Sources [11.1 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.8 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.8 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [391 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 35.1 MB in 4s (9,099 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg-2.dsc' iqtree_2.4.0+dfsg-2.dsc 2177 SHA256:35b9063fdc325c91918e90235c26c49937791f79f4e7ff177bbaabfe15855654 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg.orig.tar.xz' iqtree_2.4.0+dfsg.orig.tar.xz 2291260 SHA256:cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg-2.debian.tar.xz' iqtree_2.4.0+dfsg-2.debian.tar.xz 22260 SHA256:b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e iqtree_2.4.0+dfsg.orig.tar.xz b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 iqtree_2.4.0+dfsg-2.debian.tar.xz 35b9063fdc325c91918e90235c26c49937791f79f4e7ff177bbaabfe15855654 iqtree_2.4.0+dfsg-2.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Tue, 21 Jul 2026 10:58:59 +0000 | +------------------------------------------------------------------------------+ Rebuilding iqtree=2.4.0+dfsg-2 in /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdbaEawj/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/iqtree-2.4.0+dfsg I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [193 kB] Get:2 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable InRelease [193 kB] Get:3 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable InRelease [193 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages [10.6 MB] Get:5 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 Packages [10.6 MB] Get:6 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 Packages [10.6 MB] Fetched 32.4 MB in 3s (10.8 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260712T202631Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20260715T144045Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.13-stable-1 [60.9 kB] Fetched 60.9 kB in 0s (5861 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0cb__4r/libevent-openssl-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 7.1.3-1 [1963 kB] Fetched 1963 kB in 0s (104 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf1gwmrfw/linux-libc-dev_7.1.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (11.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp95szdqy3/gzip_1.13-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libtsan2 amd64 16.1.0-2 [2573 kB] Fetched 2573 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjwumz7h8/libtsan2_16.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.3.0-1 [12.8 MB] Fetched 12.8 MB in 0s (153 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3nzm3qek/gfortran-15-x86-64-linux-gnu_15.3.0-1_amd64.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/tmpw98i5yb9/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b2 [670 kB] Fetched 670 kB in 0s (50.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvptnn947/libpmix2t64_6.0.0+really5.0.9-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42.2-2 [215 kB] Fetched 215 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp34ys6e6s/libmount1_2.42.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (41.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp41chx2pr/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Fetched 58.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp104610b3/libelf1t64_0.195-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.2.0-2 [43.2 kB] Fetched 43.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdtp60fs9/libmd0_1.2.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Fetched 132 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7bbmtzcr/libbsd0_0.12.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ug36ohq/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.4-1 [16.2 MB] Fetched 16.2 MB in 0s (168 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxfidf3ax/cmake_4.3.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Fetched 1034 kB in 0s (80.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp32zb2h5w/libeigen3-dev_3.4.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5+b1 [1568 B] Fetched 1568 B in 0s (135 kB/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmplvw0my5o/cpp_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Fetched 716 kB in 0s (57.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1vpsve4l/libfabric1_2.1.0-1.1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Fetched 795 kB in 0s (67.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkhft85f5/libze1_1.28.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-8 [66.9 kB] Fetched 66.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsbj7kp46/libpam0g_1.7.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB] Fetched 422 kB in 0s (38.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6kkysf6t/libcurl4t64_8.21.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2+b1 [62.2 kB] Fetched 62.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyuch3ci2/libnl-3-200_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b2 [560 kB] Fetched 560 kB in 0s (47.4 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpmbrcoq9g/libgmp10_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (30.1 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmpg_kb0vn1/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (5383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjew1ifgx/base-passwd_3.6.8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-3 [729 kB] Fetched 729 kB in 0s (49.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpalhkses2/libmpfr6_4.2.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2+b1 [105 kB] Fetched 105 kB in 0s (9854 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb5468k8j/libnl-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Fetched 220 kB in 0s (21.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpngse0bdp/libnl-route-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (77.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiyr2lvif/dpkg-dev_1.23.7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 openssh-common amd64 1:10.4p1-1 [481 kB] Fetched 481 kB in 0s (38.3 MB/s) dpkg-name: info: moved 'openssh-common_1%3a10.4p1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpp4hhv3qc/openssh-common_10.4p1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0hki_a29/gettext-base_1.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42.2-2 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1cvpsgtd/libsmartcols1_2.42.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 libyaml-cpp-dev amd64 0.9.0+dfsg-5 [188 kB] Fetched 188 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy8atky4z/libyaml-cpp-dev_0.9.0+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (1655 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpta5rz8hd/pkg-config_2.5.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.3.0-1 [13.2 MB] Fetched 13.2 MB in 0s (162 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_dwkpv6/g++-15-x86-64-linux-gnu_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Fetched 47.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcdkdpl42/libpkgconf7_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsprng2-dev amd64 2.0a-19 [79.3 kB] Fetched 79.3 kB in 0s (7404 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprfw79tly/libsprng2-dev_2.0a-19_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 googletest all 1.17.0-1 [522 kB] Fetched 522 kB in 0s (39.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpppdwy2fd/googletest_1.17.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Fetched 6020 B in 0s (586 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_s7uxarv/dh-strip-nondeterminism_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.283 [7572 B] Fetched 7572 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7rsb5e8p/libdebconfclient0_0.283_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 openssh-client amd64 1:10.4p1-1 [720 kB] Fetched 720 kB in 0s (52.1 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.4p1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpb8hj8jru/openssh-client_10.4p1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 g++-15 amd64 15.3.0-1 [28.7 kB] Fetched 28.7 kB in 0s (2583 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qxtcb6u/g++-15_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvu5bkacb/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (27.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoqfm0ld8/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Fetched 1336 kB in 0s (85.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp061msn31/groff-base_1.24.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.6.0-1 [24.7 kB] Fetched 24.7 kB in 0s (2315 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.6.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpa5auz5f6/libattr1_2.6.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Fetched 50.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmp51056yv7/libxext6_1.3.4-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-17 [1790 kB] Fetched 1790 kB in 0s (77.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ixgak47/libc6_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-3 [52.2 kB] Fetched 52.2 kB in 0s (308 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjtnv1dbm/libmpc3_1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpasbxs116/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-4 [700 kB] Fetched 700 kB in 0s (55.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi21f2saa/findutils_4.10.0-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Fetched 244 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk7llxe8g/libssh2-1t64_1.11.1-4_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/tmpm9eq6can/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Fetched 345 kB in 0s (28.1 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpyiw407ip/libmagic-mgc_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Fetched 109 kB in 0s (9305 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpci6uk9s0/dwz_0.17-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgfortran-15-dev amd64 15.3.0-1 [877 kB] Fetched 877 kB in 0s (62.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvaok2law/libgfortran-15-dev_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-8 [1677 kB] Fetched 1677 kB in 0s (95.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzkn9fs7j/perl-base_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b2 [39.9 kB] Fetched 39.9 kB in 0s (2781 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ofi0_m5/libbz2-1.0_1.0.8-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261.1-3 [2566 kB] Fetched 2566 kB in 0s (94.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ccxdjzl/libsystemd-shared_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20260608-2 [137 kB] Fetched 137 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaac7il2a/libncursesw6_6.6+20260608-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.52.1-4 [158 kB] Fetched 158 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplbl6umoi/libuv1t64_1.52.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42.2-2 [1230 kB] Fetched 1230 kB in 0s (74.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz8rg3nho/util-linux_2.42.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.3.0-1 [12.1 MB] Fetched 12.1 MB in 0s (165 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuon27ooe/cpp-15-x86-64-linux-gnu_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Fetched 111 kB in 0s (9017 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpgunak8yw/libmagic1t64_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-2 [103 kB] Fetched 103 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9knr6cqp/libfuse3-4_3.18.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Fetched 1028 kB in 0s (78.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9me_88bu/libopenmpi-dev_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libubsan1 amd64 16.1.0-2 [1136 kB] Fetched 1136 kB in 0s (82.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjaok0_za/libubsan1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Fetched 451 kB in 0s (39.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo545nlrb/libprrte3_3.0.13-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Fetched 877 kB in 0s (67.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprs9i45qe/libgfortran5_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Fetched 13.9 MB in 0s (158 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxk59yyj1/libamd-comgr3_7.0.2+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.13+dfsg-1 [188 kB] Fetched 188 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5zkr1bf/libldap2_2.6.13+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.4-1 [63.4 kB] Fetched 63.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_4rbx7n3/rpcsvc-proto_1.4.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.13-stable-1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp699a696b/libevent-core-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 cpp-15 amd64 15.3.0-1 [1280 B] Fetched 1280 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3atstatc/cpp-15_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5+b1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpqpkxjowe/g++_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7y7jyisp/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB] Fetched 8644 kB in 0s (167 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd1sirhqt/libz3-4_4.13.3-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libhwasan0 amd64 16.1.0-2 [1580 kB] Fetched 1580 kB in 0s (97.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjquo19wx/libhwasan0_16.1.0-2_amd64.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/tmprmglw558/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpc1v68fbk/libaudit-common_4.1.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libctf-nobfd0 amd64 2.46.50.20260617-1 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5kwnn0ku/libctf-nobfd0_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Fetched 183 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphl6wq1dk/libevent-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-5 [109 kB] Fetched 109 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5g_b3vtr/libidn2-0_2.3.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.8-2 [362 kB] Fetched 362 kB in 0s (35.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphdk8cjlv/libarchive13t64_3.8.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.13-stable-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3b0u9xqr/libevent-dev_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Fetched 9348 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvtuddoqs/libkeyutils1_1.6.3-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.3-1 [332 kB] Fetched 332 kB in 0s (33.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_0s3qtz6/liblzma5_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Fetched 49.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxw7ygrkj/libpipeline1_1.5.8-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libasan8 amd64 16.1.0-2 [2889 kB] Fetched 2889 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4er_p42/libasan8_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Fetched 20.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpuoaaty7s/libxau6_1.0.11-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils-common amd64 2.46.50.20260617-1 [2636 kB] Fetched 2636 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp37xqawn_/binutils-common_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (67.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj57_xaj8/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-11 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmiyua5wo/libltdl-dev_2.5.4-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7_pbwdm8/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libsframe3 amd64 2.46.50.20260617-1 [84.7 kB] Fetched 84.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnxcav2l2/libsframe3_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b4 [28.2 MB] Fetched 28.2 MB in 0s (185 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpjsiz8vyu/libllvm21_21.1.8-7+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4w_nx52q/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-8 [246 kB] Fetched 246 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2f1b0sn/libpam-runtime_1.7.0-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1.1+b1 [135 kB] Fetched 135 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9k917y91/librhash1_1.4.6-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Fetched 516 kB in 0s (48.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_a2rt3n/autoconf_2.73-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b2 [27.1 kB] Fetched 27.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2hp3x63/libxxhash0_0.8.3-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-2 [166 kB] Fetched 166 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph7r11xyr/libhwloc15_2.14.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b2 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpihymf87d/libnuma-dev_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-2 [383 kB] Fetched 383 kB in 0s (37.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoyx4huya/ibverbs-providers_63.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libitm1 amd64 16.1.0-2 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiyxtflzx/libitm1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Fetched 3654 kB in 0s (142 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyl1ug6s9/libprrte-dev_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Fetched 121 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkq650pbk/libexpat1_2.8.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1+b1 [305 kB] Fetched 305 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhq6qib1/libnettle8t64_3.10.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rnu6oku/libngtcp2-16_1.22.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-3 [51.9 kB] Fetched 51.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyzcas2rs/libprrte-bin_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.3-1+b1 [18.2 kB] Fetched 18.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptijlwfyt/libcap-ng0_0.9.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.3-1 [740 kB] Fetched 740 kB in 0s (61.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9dk5c73e/xz-utils_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Fetched 328 kB in 0s (0 B/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpenogu57w/libgmpxx4ldbl_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Fetched 918 kB in 0s (69.9 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp3ra58sas/zlib1g-dev_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Fetched 320 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpet2_7fle/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14.2 [88.0 kB] Fetched 88.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgtrsgeua/base-files_14.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15-base amd64 15.3.0-1 [37.4 kB] Fetched 37.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8y9pqmzn/gcc-15-base_15.3.0-1_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/tmppd_7ndeb/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Fetched 2018 kB in 0s (75.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphkt8o8zv/libopenmpi40_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgomp1 amd64 16.1.0-2 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7nmibgxq/libgomp1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20260608-2 [276 kB] Fetched 276 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0h4rv52/ncurses-base_6.6+20260608-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sysvinit-utils amd64 3.18-1 [29.7 kB] Fetched 29.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptps12cgf/sysvinit-utils_3.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-2 [71.8 kB] Fetched 71.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpksgknsmm/librdmacm1t64_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-11 [55.2 kB] Fetched 55.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp73nf719f/libsasl2-2_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260302-1 [142 kB] Fetched 142 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpemswh__x/mawk_1.3.4.20260302-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (71.1 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmp7y2xol_s/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 time amd64 1.10-0.1 [58.4 kB] Fetched 58.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_76t2c43/time_1.10-0.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.6.3-1 [2488 kB] Fetched 2488 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpenm7nezv/libssl3t64_3.6.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpoawnk5d_/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1+b1 [96.4 kB] Fetched 96.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp1nrw3wtg/libcrypt1_4.5.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b2 [77.7 kB] Fetched 77.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphld531q8/libgdbm6t64_1.26-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-3 [23.3 kB] Fetched 23.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbya57p1z/libdrm-amdgpu1_2.4.134-3_amd64.deb' Downloading dependency 1 of 263: libevent-openssl-2.1-7t64:amd64=2.1.13-stable-1 Downloading dependency 2 of 263: linux-libc-dev:amd64=7.1.3-1 Downloading dependency 3 of 263: gzip:amd64=1.13-1 Downloading dependency 4 of 263: libtsan2:amd64=16.1.0-2 Downloading dependency 5 of 263: gfortran-15-x86-64-linux-gnu:amd64=15.3.0-1 Downloading dependency 6 of 263: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 7 of 263: libpmix2t64:amd64=6.0.0+really5.0.9-3+b2 Downloading dependency 8 of 263: libmount1:amd64=2.42.2-2 Downloading dependency 9 of 263: make:amd64=4.4.1-3 Downloading dependency 10 of 263: libelf1t64:amd64=0.195-1 Downloading dependency 11 of 263: libmd0:amd64=1.2.0-2 Downloading dependency 12 of 263: libbsd0:amd64=0.12.2-3 Downloading dependency 13 of 263: init-system-helpers:amd64=1.69 Downloading dependency 14 of 263: cmake:amd64=4.3.4-1 Downloading dependency 15 of 263: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 16 of 263: cpp:amd64=4:15.2.0-5+b1 Downloading dependency 17 of 263: libfabric1:amd64=2.1.0-1.1+b2 Downloading dependency 18 of 263: libze1:amd64=1.28.2-2 Downloading dependency 19 of 263: libpam0g:amd64=1.7.0-8 Downloading dependency 20 of 263: libcurl4t64:amd64=8.21.0-2 Downloading dependency 21 of 263: libnl-3-200:amd64=3.12.0-2+b1 Downloading dependency 22 of 263: libgmp10:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 23 of 263: libx11-data:amd64=2:1.8.13-1 Downloading dependency 24 of 263: base-passwd:amd64=3.6.8 Downloading dependency 25 of 263: libmpfr6:amd64=4.2.2-3 Downloading dependency 26 of 263: libnl-3-dev:amd64=3.12.0-2+b1 Downloading dependency 27 of 263: libnl-route-3-dev:amd64=3.12.0-2+b1 Downloading dependency 28 of 263: dpkg-dev:amd64=1.23.7 Downloading dependency 29 of 263: openssh-common:amd64=1:10.4p1-1 Downloading dependency 30 of 263: gettext-base:amd64=1.0-3 Downloading dependency 31 of 263: libsmartcols1:amd64=2.42.2-2 Downloading dependency 32 of 263: libyaml-cpp-dev:amd64=0.9.0+dfsg-5 Downloading dependency 33 of 263: pkg-config:amd64=2.5.1-4 Downloading dependency 34 of 263: g++-15-x86-64-linux-gnu:amd64=15.3.0-1 Downloading dependency 35 of 263: libpkgconf7:amd64=2.5.1-4 Downloading dependency 36 of 263: libsprng2-dev:amd64=2.0a-19 Downloading dependency 37 of 263: googletest:amd64=1.17.0-1 Downloading dependency 38 of 263: dh-strip-nondeterminism:amd64=1.15.1-1 Downloading dependency 39 of 263: libdebconfclient0:amd64=0.283 Downloading dependency 40 of 263: openssh-client:amd64=1:10.4p1-1 Downloading dependency 41 of 263: g++-15:amd64=15.3.0-1 Downloading dependency 42 of 263: pkgconf:amd64=2.5.1-4 Downloading dependency 43 of 263: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 44 of 263: groff-base:amd64=1.24.1-1 Downloading dependency 45 of 263: libattr1:amd64=1:2.6.0-1 Downloading dependency 46 of 263: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 47 of 263: libc6:amd64=2.42-17 Downloading dependency 48 of 263: libmpc3:amd64=1.3.1-3 Downloading dependency 49 of 263: dh-autoreconf:amd64=22 Downloading dependency 50 of 263: findutils:amd64=4.10.0-4 Downloading dependency 51 of 263: libssh2-1t64:amd64=1.11.1-4 Downloading dependency 52 of 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Downloading dependency 100 of 263: libxxhash0:amd64=0.8.3-2+b2 Downloading dependency 101 of 263: libhwloc15:amd64=2.14.0-2 Downloading dependency 102 of 263: libnuma-dev:amd64=2.0.19-1+b2 Downloading dependency 103 of 263: ibverbs-providers:amd64=63.0-2 Downloading dependency 104 of 263: libitm1:amd64=16.1.0-2 Downloading dependency 105 of 263: libprrte-dev:amd64=3.0.13-3 Downloading dependency 106 of 263: libexpat1:amd64=2.8.2-1 Downloading dependency 107 of 263: libnettle8t64:amd64=3.10.2-1+b1 Downloading dependency 108 of 263: libngtcp2-16:amd64=1.22.1-1 Downloading dependency 109 of 263: libprrte-bin:amd64=3.0.13-3 Downloading dependency 110 of 263: libcap-ng0:amd64=0.9.3-1+b1 Downloading dependency 111 of 263: xz-utils:amd64=5.8.3-1 Downloading dependency 112 of 263: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 113 of 263: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 114 of 263: libbrotli1:amd64=1.2.0-3 Downloading dependency 115 of 263: base-files:amd64=14.2 Downloading dependency 116 of 263: gcc-15-base:amd64=15.3.0-1 Downloading dependency 117 of 263: help2man:amd64=1.49.3 Downloading dependency 118 of 263: libopenmpi40:amd64=5.0.10-1 Downloading dependency 119 of 263: libgomp1:amd64=16.1.0-2 Downloading dependency 120 of 263: ncurses-base:amd64=6.6+20260608-2 Downloading dependency 121 of 263: sysvinit-utils:amd64=3.18-1 Downloading dependency 122 of 263: librdmacm1t64:amd64=63.0-2 Downloading dependency 123 of 263: libsasl2-2:amd64=2.1.28+dfsg1-11 Downloading dependency 124 of 263: mawk:amd64=1.3.4.20260302-1 Downloading dependency 125 of 263: automake:amd64=1:1.18.1-4 Downloading dependency 126 of 263: time:amd64=1.10-0.1 Downloading dependency 127 of 263: libssl3t64:amd64=3.6.3-1 Downloading dependency 128 of 263: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 129 of 263: libcrypt1:amd64=1:4.5.1-1+b1 Downloading dependency 130 of 263: libgdbm6t64:amd64=1.26-1+b2 Downloading dependency 131 of 263: libdrm-amdgpu1:amd64=2.4.134-3 Downloading dependency 132 of 263: libcom-err2:amd64=1.47.4-1Get:1 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Fetched 19.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp291lvdqe/libcom-err2_1.47.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Fetched 2658 kB in 0s (126 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvp19h83i/gettext_1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgcc-15-dev amd64 15.3.0-1 [2718 kB] Fetched 2718 kB in 0s (124 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4pjuo2qj/libgcc-15-dev_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Fetched 335 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1f44n2t0/libkrb5-3_1.22.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-2 [99.8 kB] Fetched 99.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo7vo_g1v/bsdextrautils_2.42.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libstdc++6 amd64 16.1.0-2 [822 kB] Fetched 822 kB in 0s (64.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_vluhgi2/libstdc++6_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Fetched 500 kB in 0s (40.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp44wm4ske/libsimde-dev_0.8.4~rc3-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b2 [52.0 kB] Fetched 52.0 kB in 0s (4796 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4glajrj7/libgdbm-compat4t64_1.26-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Fetched 28.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpckfjlfy0/libxdmcp6_1.1.5-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Fetched 3504 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpisnw7byh/mpi-default-dev_1.20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46.50.20260617-1 [1077 kB] Fetched 1077 kB in 0s (77.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps8z89vml/binutils-x86-64-linux-gnu_2.46.50.20260617-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z 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/tmpwvtbm_l7/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils amd64 2.46.50.20260617-1 [282 kB] Fetched 282 kB in 0s (24.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9y335h6c/binutils_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-8 [4344 kB] Fetched 4344 kB in 0s (146 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0y4lpy87/libperl5.40_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-2 [260 kB] Fetched 260 kB in 0s (24.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqa40hzx/libhwloc-dev_2.14.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-8 [46.3 kB] Fetched 46.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmproh3wn29/libpam-modules-bin_1.7.0-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libstdc++-15-dev amd64 15.3.0-1 [2784 kB] Fetched 2784 kB in 0s (92.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpabd19pfq/libstdc++-15-dev_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261.1-3 [3327 kB] Fetched 3327 kB in 0s (132 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeo9dgpbb/systemd_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 261.1-3 [467 kB] Fetched 467 kB in 0s (43.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr9mwk4h7/libsystemd0_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (39.4 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpq3c04crm/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Fetched 31.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeuy5k3rb/libkrb5support0_1.22.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (99.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9gcl_mpm/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.8.0-2 [345 kB] Fetched 345 kB in 0s (33.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsxmnfnvq/libucc1_1.8.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Fetched 60.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphuzh8rzn/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Fetched 829 kB in 0s (66.0 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpvayk6p54/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.8-2 [87.5 kB] Fetched 87.5 kB in 0s (7474 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0pe9t8tz/libjsoncpp26_1.9.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgcc-s1 amd64 16.1.0-2 [74.1 kB] Fetched 74.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmt3v7neu/libgcc-s1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b2 [297 kB] Fetched 297 kB in 0s (28.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprkr0ercf/libpcre2-8-0_10.46-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Fetched 17.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpscfhiqk8/libsasl2-modules-db_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Fetched 80.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwj7wvq80/libfido2-1_1.17.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.4.0-1 [37.1 kB] Fetched 37.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz8xlj4uw/libacl1_2.4.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Fetched 934 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpemdnofmt/debhelper_14.3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [1204 B] Fetched 1204 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5bsqaz_c/g++-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Fetched 480 kB in 0s (45.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwi5jhluk/libunistring5_1.4.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-16-base amd64 16.1.0-2 [36.8 kB] Fetched 36.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnyf2zpzx/gcc-16-base_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2+b1 [200 kB] Fetched 200 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3d2ksd2k/libnl-route-3-200_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Fetched 416 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4jfyzbr3/libltdl7_2.5.4-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [1440 B] Fetched 1440 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpy9vluef3/gcc-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyymu3oaq/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.11-2 [87.3 kB] Fetched 87.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkpe7bwlx/libselinux1_3.11-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42.2-2 [173 kB] Fetched 173 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfm5mt2y1/libblkid1_2.42.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-3 [38.5 kB] Fetched 38.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfzk01_qz/libdrm2_2.4.134-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.13-stable-1 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30vvmuc3/libevent-extra-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Fetched 14.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkkdt_cdz/libxnvctrl0_535.171.04-1+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-2 [28.5 kB] Fetched 28.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpikw4ti8i/libibumad3_63.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 libyaml-cpp0.9 amd64 0.9.0+dfsg-5 [147 kB] Fetched 147 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgfh7lmc_/libyaml-cpp0.9_0.9.0+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42.2-2 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz2_wdhxk/libuuid1_2.42.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (47.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu9t1vs56/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Fetched 642 kB in 0s (56.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3s8vpe7m/libxml2-16_2.15.3+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-2 [21.7 kB] Fetched 21.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzc6we4no/libhwloc-plugins_2.14.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Fetched 69.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqmp9mto/libuchardet0_0.0.8-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-10 [14.9 kB] Fetched 14.9 kB in 0s (1434 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0e2e1thf/liblocale-gettext-perl_1.07-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-17 [620 kB] Fetched 620 kB in 0s (50.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppylvepq7/libc-bin_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Fetched 89.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnns51n6f/libnghttp2-14_1.69.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-2 [43.2 kB] Fetched 43.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppqkxj1j7/libibmad5_63.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.3.0-1 [23.4 MB] Fetched 23.4 MB in 0s (190 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kisswbe/gcc-15-x86-64-linux-gnu_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (93.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbd1jf41k/dpkg_1.23.7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.7.1-2 [30.5 kB] Fetched 30.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwm8gtfu8/libffi8_3.7.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-2 [62.8 kB] Fetched 62.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8oab0ejt/libibverbs1_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-8 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp020qhuig/libpam-modules_1.7.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [4644 B] Fetched 4644 B in 0s (463 kB/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpyvysv6ry/cpp-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpybty7hj9/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20260608-2 [445 kB] Fetched 445 kB in 0s (43.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8s75xolg/ncurses-bin_6.6+20260608-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b2 [305 kB] Fetched 305 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqnp71gmh/libzstd1_1.5.7+dfsg-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Fetched 9385 kB in 0s (157 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2386b1_u/libamdhip64-6_6.4.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libucx0 amd64 1.22.0~rc1-1 [1015 kB] Fetched 1015 kB in 0s (77.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq6anb93o/libucx0_1.22.0~rc1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg4kf6v8s/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.6-2 [983 kB] Fetched 983 kB in 0s (73.9 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.6-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpzaxnfdi6/procps_4.0.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libatomic1 amd64 16.1.0-2 [10.4 kB] Fetched 10.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp98wdkryw/libatomic1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-17 [1991 kB] Fetched 1991 kB in 0s (108 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkdytdll9/libc6-dev_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-10 [70.3 kB] Fetched 70.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4jlsayda/liblz4-1_1.10.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-3 [1559 kB] Fetched 1559 kB in 0s (88.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi8kyum__/bash_5.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgqp283dh/coreutils_9.10-1_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/tmpwalvsxr9/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4q0fmnfu/libgssapi-krb5-2_1.22.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-17 [1097 kB] Fetched 1097 kB in 0s (70.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppr55bevn/libc-gconv-modules-extra_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Fetched 709 kB in 0s (65.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdu8r1i9f/libdb5.3t64_5.3.28+dfsg2-11+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.0-1 [60.8 kB] Fetched 60.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxquhuxpa/libpsl5t64_0.23.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20260608-2 [353 kB] Fetched 353 kB in 0s (31.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplljpu3ka/libtinfo6_6.6+20260608-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgprofng0 amd64 2.46.50.20260617-1 [821 kB] Fetched 821 kB in 0s (53.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkv6z_u5a/libgprofng0_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpppwld792/po-debconf_1.0.22_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libctf0 amd64 2.46.50.20260617-1 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30p67z11/libctf0_2.46.50.20260617-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 liblsan0 amd64 16.1.0-2 [1281 kB] Fetched 1281 kB in 0s (92.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsgn_bx9f/liblsan0_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Fetched 820 kB in 0s (68.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq3i_vdy4/autopoint_1.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-1 amd64 2:4.0.6-2 [69.2 kB] Fetched 69.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-1_2%3a4.0.6-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpte7c4k2x/libproc2-1_4.0.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libbinutils amd64 2.46.50.20260617-1 [536 kB] Fetched 536 kB in 0s (45.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppcvcj_25/libbinutils_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Fetched 11.3 MB in 0s (176 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9047qcyo/libboost1.90-dev_1.90.0-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (51.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0o1f95h1/libisl23_0.27-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Fetched 79.0 kB in 0s (7552 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplslteqft/libk5crypto3_1.22.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.15.1-1 [65.6 kB] Fetched 65.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_a6xfgrn/libjansson4_2.15.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15 amd64 15.3.0-1 [546 kB] Fetched 546 kB in 0s (41.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd3z7v9kc/gcc-15_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsprng2 amd64 2.0a-19 [76.0 kB] Fetched 76.0 kB in 0s (7161 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppdtbpia3/libsprng2_2.0a-19_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 261.1-3 [139 kB] Fetched 139 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8z1fntop/libudev1_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.19-2 [18.5 kB] Fetched 18.5 kB in 0s (1791 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2b6q8qhg/libpciaccess0_0.19-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libcc1-0 amd64 16.1.0-2 [46.1 kB] Fetched 46.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo6i80afp/libcc1-0_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdpkg-perl all 1.23.7 [669 kB] Fetched 669 kB in 0s (53.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rg_q3ip/libdpkg-perl_1.23.7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB] Fetched 23.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdjx_tmto/libngtcp2-crypto-ossl0_1.22.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.2-3 [90.9 kB] Fetched 90.9 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp7pc9ytxd/zlib1g_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Fetched 93.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17giw82d/libedit2_3.1-20260512-1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi6orp5ri/libpsm2-2_11.2.185-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.6.3-1 [320 kB] Fetched 320 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpypes0eot/openssl-provider-legacy_3.6.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-3 [7860 B] Fetched 7860 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ws14v1g/libdrm-common_2.4.134-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debianutils amd64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjhinp1_x/debianutils_5.23.2_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/tmp5dg158gz/chrpath_0.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp08dpv4zp/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pci.ids all 0.0~2026.07.06-1 [285 kB] Fetched 285 kB in 0s (28.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwmgmywg/pci.ids_0.0~2026.07.06-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-2 [695 kB] Fetched 695 kB in 0s (57.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqngll0y/libibverbs-dev_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (2366 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj5f4ts94/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1+b1 [28.6 kB] Fetched 28.6 kB in 0s (1921 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30zvgc9p/libcbor0.10_0.10.2-2.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Fetched 3064 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu4bzj6x_/libboost-dev_1.90.0.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.1-1 [49.9 kB] Fetched 49.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpal1tfst9/libseccomp2_2.6.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Fetched 43.0 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpwzfrjjt4/file_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b2 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplzkhjdfg/bzip2_1.0.8-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b4 [768 kB] Fetched 768 kB in 0s (53.9 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpq3assage/libclang-common-21-dev_21.1.8-7+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Fetched 77.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp91lxaow6/libdebhelper-perl_14.3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-8 [264 kB] Fetched 264 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4u4quvi/perl_5.40.1-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gfortran-15 amd64 15.3.0-1 [22.2 kB] Fetched 22.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_u2q15r4/gfortran-15_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-8 [3019 kB] Fetched 3019 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_46zby58/perl-modules-5.40_5.40.1-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Fetched 35.9 kB in 0s (3448 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprpirhtar/pkgconf-bin_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5+b1 [5160 B] Fetched 5160 B in 0s (493 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7yl7q47b/gcc_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Fetched 154 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyvpncb60/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libquadmath0 amd64 16.1.0-2 [148 kB] Fetched 148 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplmrq_zpi/libquadmath0_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3_yiksrj/libfile-stripnondeterminism-perl_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Fetched 641 kB in 0s (47.2 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmppffwxh07/libgmp-dev_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Fetched 678 kB in 0s (45.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbuqwbci/libhsa-runtime64-1_6.4.3+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Fetched 22.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7crizt6b/libnuma1_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1+b1 [42.8 kB] Fetched 42.8 kB in 0s (4116 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprt0gk9zm/ocl-icd-libopencl1_2.3.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8qn1e7zp/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-3 [331 kB] Fetched 331 kB in 0s (31.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp47urebh8/sed_4.9-3_amd64.deb' Downloading dependency 133 of 263: gettext:amd64=1.0-3 Downloading dependency 134 of 263: libgcc-15-dev:amd64=15.3.0-1 Downloading dependency 135 of 263: libkrb5-3:amd64=1.22.1-3 Downloading dependency 136 of 263: bsdextrautils:amd64=2.42.2-2 Downloading dependency 137 of 263: libstdc++6:amd64=16.1.0-2 Downloading dependency 138 of 263: libsimde-dev:amd64=0.8.4~rc3-5 Downloading dependency 139 of 263: libgdbm-compat4t64:amd64=1.26-1+b2 Downloading dependency 140 of 263: libxdmcp6:amd64=1:1.1.5-2+b1 Downloading dependency 141 of 263: mpi-default-dev:amd64=1.20 Downloading dependency 142 of 263: binutils-x86-64-linux-gnu:amd64=2.46.50.20260617-1 Downloading dependency 143 of 263: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 144 of 263: binutils:amd64=2.46.50.20260617-1 Downloading dependency 145 of 263: libperl5.40:amd64=5.40.1-8 Downloading dependency 146 of 263: libhwloc-dev:amd64=2.14.0-2 Downloading dependency 147 of 263: libpam-modules-bin:amd64=1.7.0-8 Downloading dependency 148 of 263: libstdc++-15-dev:amd64=15.3.0-1 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libseccomp2:amd64=2.6.1-1 Downloading dependency 243 of 263: file:amd64=1:5.47-4 Downloading dependency 244 of 263: bzip2:amd64=1.0.8-6+b2 Downloading dependency 245 of 263: libclang-common-21-dev:amd64=1:21.1.8-7+b4 Downloading dependency 246 of 263: libdebhelper-perl:amd64=14.3 Downloading dependency 247 of 263: perl:amd64=5.40.1-8 Downloading dependency 248 of 263: gfortran-15:amd64=15.3.0-1 Downloading dependency 249 of 263: perl-modules-5.40:amd64=5.40.1-8 Downloading dependency 250 of 263: pkgconf-bin:amd64=2.5.1-4 Downloading dependency 251 of 263: gcc:amd64=4:15.2.0-5+b1 Downloading dependency 252 of 263: openmpi-bin:amd64=5.0.10-1 Downloading dependency 253 of 263: libquadmath0:amd64=16.1.0-2 Downloading dependency 254 of 263: libfile-stripnondeterminism-perl:amd64=1.15.1-1 Downloading dependency 255 of 263: libgmp-dev:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 256 of 263: libhsa-runtime64-1:amd64=6.4.3+dfsg-5 Downloading dependency 257 of 263: libnuma1:amd64=2.0.19-1+b2 Downloading dependency 258 of 263: ocl-icd-libopencl1:amd64=2.3.4-1+b1 Downloading dependency 259 of 263: dash:amd64=0.5.12-12 Downloading dependency 260 of 263: sed:amd64=4.9-3 Downloading dependency 261 of 263: libevent-pthreads-2.1-7t64:amd64=2.1.13-stable-1Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.13-stable-1 [53.8 kB] Fetched 53.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplqmatqdm/libevent-pthreads-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Fetched 18.8 kB in 0s (1797 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfaai7o1u/libmunge2_0.5.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-17 [38.1 kB] Fetched 38.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphtnunyse/libc-dev-bin_2.42-17_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-buildpackage: info: host architecture amd64 dpkg-source --before-build . 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/tmpxtvpwp73/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.3Dxanp_XlY as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.3Dxanp_XlY 127.0.0.1 - - [21/Jul/2026 11:01:06] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:44449 ./ InRelease 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:44449 ./ Release [462 B] 127.0.0.1 - - [21/Jul/2026 11:01:06] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:44449 ./ Release.gpg 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:44449 ./ Packages [324 kB] Fetched 325 kB in 0s (20.8 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./gcc-16-base_16.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libc-gconv-modules-extra_2.42-17_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libc6_2.42-17_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libgcc-s1_16.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./mawk_1.3.4.20260302-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./base-files_14.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libtinfo6_6.6%2b20260608-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./bash_5.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libacl1_2.4.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libattr1_2.6.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb2_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libsmartcols1_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libudev1_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libuuid1_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./util-linux_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libdebconfclient0_0.283_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./libc-bin_2.42-17_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./ncurses-base_6.6%2b20260608-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:06] "GET /./sysvinit-utils_3.18-1_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.3Dxanp_XlY 127.0.0.1 - - [21/Jul/2026 11:01:08] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 11:01:08] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:44449 ./ InRelease 127.0.0.1 - - [21/Jul/2026 11:01:08] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:44449 ./ Release 127.0.0.1 - - [21/Jul/2026 11:01:08] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 11:01:08] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:44449 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not 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.3Dxanp_XlY usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./libsystemd-shared_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./systemd_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./libexpat1_2.8.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./liblocale-gettext-perl_1.07-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./libstdc%2b%2b6_16.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./libuchardet0_0.0.8-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:21] "GET /./groff-base_1.24.1-1_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libucc1_1.8.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./openmpi-common_5.0.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libibverbs-dev_63.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libprrte3_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libprrte-dev_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libnuma-dev_2.0.19-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libltdl7_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libltdl-dev_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libhwloc-dev_2.14.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libevent-2.1-7t64_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libevent-extra-2.1-7t64_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libevent-dev_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libprrte-bin_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./time_1.10-0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libboost1.90-dev_1.90.0-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./libboost-dev_1.90.0.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 11:01:23] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpxtvpwp73/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.3Dxanp_XlY Reading package lists... Building dependency tree... Reading state information... libevent-openssl-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-openssl-2.1-7t64 set to manually installed. linux-libc-dev is already the newest version (7.1.3-1). linux-libc-dev set to manually installed. gzip is already the newest version (1.13-1). libtsan2 is already the newest version (16.1.0-2). libtsan2 set to manually installed. gfortran-15-x86-64-linux-gnu is already the newest version (15.3.0-1). gfortran-15-x86-64-linux-gnu set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b2). libpmix2t64 set to manually installed. libmount1 is already the newest version (2.42.2-2). make is already the newest version (4.4.1-3). make set to manually installed. libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. libmd0 is already the newest version (1.2.0-2). libbsd0 is already the newest version (0.12.2-3). libbsd0 set to manually installed. init-system-helpers is already the newest version (1.69). cmake is already the newest version (4.3.4-1). cmake set to manually installed. libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. libpam0g is already the newest version (1.7.0-8). libcurl4t64 is already the newest version (8.21.0-2). libcurl4t64 set to manually installed. libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b2). libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. base-passwd is already the newest version (3.6.8). libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. libnl-route-3-dev is already the newest version (3.12.0-2+b1). libnl-route-3-dev set to manually installed. dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. openssh-common is already the newest version (1:10.4p1-1). openssh-common set to manually installed. gettext-base is already the newest version (1.0-3). gettext-base set to manually installed. libsmartcols1 is already the newest version (2.42.2-2). libyaml-cpp-dev is already the newest version (0.9.0+dfsg-5). libyaml-cpp-dev set to manually installed. pkg-config is already the newest version (2.5.1-4). pkg-config set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.3.0-1). g++-15-x86-64-linux-gnu set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. googletest is already the newest version (1.17.0-1). googletest set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.1-1). dh-strip-nondeterminism set to manually installed. libdebconfclient0 is already the newest version (0.283). openssh-client is already the newest version (1:10.4p1-1). openssh-client set to manually installed. g++-15 is already the newest version (15.3.0-1). g++-15 set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. libjs-jquery is already the newest version (3.7.1+dfsg+~3.5.33-1). libjs-jquery set to manually installed. groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. libattr1 is already the newest version (1:2.6.0-1). libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libc6 is already the newest version (2.42-17). libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. findutils is already the newest version (4.10.0-4). libssh2-1t64 is already the newest version (1.11.1-4). libssh2-1t64 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libmagic-mgc is already the newest version (1:5.47-4). libmagic-mgc set to manually installed. dwz is already the newest version (0.17-1). dwz set to manually installed. libgfortran-15-dev is already the newest version (15.3.0-1). libgfortran-15-dev set to manually installed. perl-base is already the newest version (5.40.1-8). libbz2-1.0 is already the newest version (1.0.8-6+b2). libsystemd-shared is already the newest version (261.1-3). libsystemd-shared set to manually installed. libncursesw6 is already the newest version (6.6+20260608-2). libncursesw6 set to manually installed. libuv1t64 is already the newest version (1.52.1-4). libuv1t64 set to manually installed. util-linux is already the newest version (2.42.2-2). cpp-15-x86-64-linux-gnu is already the newest version (15.3.0-1). cpp-15-x86-64-linux-gnu set to manually installed. libmagic1t64 is already the newest version (1:5.47-4). libmagic1t64 set to manually installed. libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. libubsan1 is already the newest version (16.1.0-2). libubsan1 set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. libgfortran5 is already the newest version (16.1.0-2). libgfortran5 set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. libldap2 is already the newest version (2.6.13+dfsg-1). libldap2 set to manually installed. rpcsvc-proto is already the newest version (1.4.4-1). rpcsvc-proto set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-core-2.1-7t64 set to manually installed. cpp-15 is already the newest version (15.3.0-1). cpp-15 set to manually installed. g++ is already the newest version (4:15.2.0-5+b1). g++ set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libz3-4 is already the newest version (4.13.3-1.1). libz3-4 set to manually installed. libhwasan0 is already the newest version (16.1.0-2). libhwasan0 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libctf-nobfd0 is already the newest version (2.46.50.20260617-1). libctf-nobfd0 set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-2.1-7t64 set to manually installed. libidn2-0 is already the newest version (2.3.8-5). libidn2-0 set to manually installed. libarchive13t64 is already the newest version (3.8.8-2). libarchive13t64 set to manually installed. libevent-dev is already the newest version (2.1.13-stable-1). libevent-dev set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. liblzma5 is already the newest version (5.8.3-1). libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. libasan8 is already the newest version (16.1.0-2). libasan8 set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. binutils-common is already the newest version (2.46.50.20260617-1). binutils-common set to manually installed. tar is already the newest version (1.35+dfsg-4). libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. libsframe3 is already the newest version (2.46.50.20260617-1). libsframe3 set to manually installed. libllvm21 is already the newest version (1:21.1.8-7+b4). libllvm21 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. libpam-runtime is already the newest version (1.7.0-8). librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. autoconf is already the newest version (2.73-2). autoconf set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. libhwloc15 is already the newest version (2.14.0-2). libhwloc15 set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. ibverbs-providers is already the newest version (63.0-2). ibverbs-providers set to manually installed. libitm1 is already the newest version (16.1.0-2). libitm1 set to manually installed. libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. libexpat1 is already the newest version (2.8.2-1). libexpat1 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libcap-ng0 is already the newest version (0.9.3-1+b1). xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b2). libgmpxx4ldbl set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.2-3). zlib1g-dev set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. base-files is already the newest version (14.2). gcc-15-base is already the newest version (15.3.0-1). gcc-15-base set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libgomp1 is already the newest version (16.1.0-2). libgomp1 set to manually installed. ncurses-base is already the newest version (6.6+20260608-2). sysvinit-utils is already the newest version (3.18-1). librdmacm1t64 is already the newest version (63.0-2). librdmacm1t64 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. mawk is already the newest version (1.3.4.20260302-1). automake is already the newest version (1:1.18.1-4). automake set to manually installed. time is already the newest version (1.10-0.1). time set to manually installed. libssl3t64 is already the newest version (3.6.3-1). libaudit1 is already the newest version (1:4.1.2-1+b1). libcrypt1 is already the newest version (1:4.5.1-1+b1). libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.134-3). libdrm-amdgpu1 set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. gettext is already the newest version (1.0-3). gettext set to manually installed. libgcc-15-dev is already the newest version (15.3.0-1). libgcc-15-dev set to manually installed. libkrb5-3 is already the newest version (1.22.1-3). libkrb5-3 set to manually installed. bsdextrautils is already the newest version (2.42.2-2). bsdextrautils set to manually installed. libstdc++6 is already the newest version (16.1.0-2). libstdc++6 set to manually installed. libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46.50.20260617-1). binutils-x86-64-linux-gnu set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. binutils is already the newest version (2.46.50.20260617-1). binutils set to manually installed. libperl5.40 is already the newest version (5.40.1-8). libperl5.40 set to manually installed. libhwloc-dev is already the newest version (2.14.0-2). libhwloc-dev set to manually installed. libpam-modules-bin is already the newest version (1.7.0-8). libstdc++-15-dev is already the newest version (15.3.0-1). libstdc++-15-dev set to manually installed. systemd is already the newest version (261.1-3). systemd set to manually installed. libsystemd0 is already the newest version (261.1-3). diffutils is already the newest version (1:3.12-1). libkrb5support0 is already the newest version (1.22.1-3). libkrb5support0 set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. libucc1 is already the newest version (1.8.0-2). libucc1 set to manually installed. autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libjsoncpp26 is already the newest version (1.9.8-2). libjsoncpp26 set to manually installed. libgcc-s1 is already the newest version (16.1.0-2). libpcre2-8-0 is already the newest version (10.46-1+b2). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. libacl1 is already the newest version (2.4.0-1). debhelper is already the newest version (14.3). debhelper set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5+b1). g++-x86-64-linux-gnu set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. gcc-16-base is already the newest version (16.1.0-2). libnl-route-3-200 is already the newest version (3.12.0-2+b1). libnl-route-3-200 set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5+b1). gcc-x86-64-linux-gnu set to manually installed. grep is already the newest version (3.12-1). libselinux1 is already the newest version (3.11-2). libblkid1 is already the newest version (2.42.2-2). libdrm2 is already the newest version (2.4.134-3). libdrm2 set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-extra-2.1-7t64 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. libibumad3 is already the newest version (63.0-2). libibumad3 set to manually installed. libyaml-cpp0.9 is already the newest version (0.9.0+dfsg-5). libyaml-cpp0.9 set to manually installed. libuuid1 is already the newest version (2.42.2-2). libtool is already the newest version (2.5.4-11). libtool set to manually installed. libxml2-16 is already the newest version (2.15.3+dfsg-1). libxml2-16 set to manually installed. libhwloc-plugins is already the newest version (2.14.0-2). libhwloc-plugins set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-10). liblocale-gettext-perl set to manually installed. libc-bin is already the newest version (2.42-17). libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. libibmad5 is already the newest version (63.0-2). libibmad5 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.3.0-1). gcc-15-x86-64-linux-gnu set to manually installed. dpkg is already the newest version (1.23.7). libffi8 is already the newest version (3.7.1-2). libffi8 set to manually installed. libibverbs1 is already the newest version (63.0-2). libibverbs1 set to manually installed. libpam-modules is already the newest version (1.7.0-8). cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5+b1). cpp-x86-64-linux-gnu set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. ncurses-bin is already the newest version (6.6+20260608-2). libzstd1 is already the newest version (1.5.7+dfsg-3+b2). libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libucx0 is already the newest version (1.22.0~rc1-1). libucx0 set to manually installed. debconf is already the newest version (1.5.92). procps is already the newest version (2:4.0.6-2). procps set to manually installed. libatomic1 is already the newest version (16.1.0-2). libatomic1 set to manually installed. libc6-dev is already the newest version (2.42-17). libc6-dev set to manually installed. liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. bash is already the newest version (5.3-3). coreutils is already the newest version (9.10-1). hostname is already the newest version (3.25). libgssapi-krb5-2 is already the newest version (1.22.1-3). libgssapi-krb5-2 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-17). libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). libpsl5t64 is already the newest version (0.23.0-1). libpsl5t64 set to manually installed. libtinfo6 is already the newest version (6.6+20260608-2). libgprofng0 is already the newest version (2.46.50.20260617-1). libgprofng0 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libctf0 is already the newest version (2.46.50.20260617-1). libctf0 set to manually installed. liblsan0 is already the newest version (16.1.0-2). liblsan0 set to manually installed. autopoint is already the newest version (1.0-3). autopoint set to manually installed. libproc2-1 is already the newest version (2:4.0.6-2). libproc2-1 set to manually installed. libbinutils is already the newest version (2.46.50.20260617-1). libbinutils set to manually installed. libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libk5crypto3 is already the newest version (1.22.1-3). libk5crypto3 set to manually installed. libjansson4 is already the newest version (2.15.1-1). libjansson4 set to manually installed. gcc-15 is already the newest version (15.3.0-1). gcc-15 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. libudev1 is already the newest version (261.1-3). libpciaccess0 is already the newest version (0.19-2). libpciaccess0 set to manually installed. libcc1-0 is already the newest version (16.1.0-2). libcc1-0 set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.22.1-1). libngtcp2-crypto-ossl0 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libedit2 is already the newest version (3.1-20260512-1). libedit2 set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. openssl-provider-legacy is already the newest version (3.6.3-1). libdrm-common is already the newest version (2.4.134-3). libdrm-common set to manually installed. debianutils is already the newest version (5.23.2). chrpath is already the newest version (0.18-1). chrpath set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. pci.ids is already the newest version (0.0~2026.07.06-1). pci.ids set to manually installed. libibverbs-dev is already the newest version (63.0-2). libibverbs-dev set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. libseccomp2 is already the newest version (2.6.1-1). libseccomp2 set to manually installed. file is already the newest version (1:5.47-4). file set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7+b4). libclang-common-21-dev set to manually installed. libdebhelper-perl is already the newest version (14.3). libdebhelper-perl set to manually installed. perl is already the newest version (5.40.1-8). perl set to manually installed. gfortran-15 is already the newest version (15.3.0-1). gfortran-15 set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-8). perl-modules-5.40 set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. gcc is already the newest version (4:15.2.0-5+b1). gcc set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. libquadmath0 is already the newest version (16.1.0-2). libquadmath0 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.1-1). libfile-stripnondeterminism-perl set to manually installed. libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b2). libgmp-dev set to manually installed. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. dash is already the newest version (0.5.12-12). sed is already the newest version (4.9-3). libevent-pthreads-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-pthreads-2.1-7t64 set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libc-dev-bin is already the newest version (2.42-17). libc-dev-bin set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.3Dxanp_XlY (Reading database ... 41292 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.3Dxanp_XlY I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.3Dxanp_XlY I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... 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.3Dxanp_XlY... I: success in 90.7516 seconds Downloading dependency 262 of 263: libmunge2:amd64=0.5.18-1 Downloading dependency 263 of 263: libc-dev-bin:amd64=2.42-17 env --chdir=/srv/rebuilderd/tmp/rebuilderdbaEawj/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1784059727 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildUgmYZz/debrebuild.sbuildrc.q_2DEmSbKugA sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --binNMU-changelog= iqtree (2.4.0+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 -- all / amd64 / i386 Build Daemon (x86-grnet-03) Tue, 14 Jul 2026 20:08:47 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildUgmYZz/debrebuild.tar.wTud8jq0Ip3B --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=iqtree-2.4.0+dfsg /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2.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 2.4.0+dfsg-2+b1 (amd64) Tue, 21 Jul 2026 11:02:37 +0000 | +==============================================================================+ Package: iqtree Version: 2.4.0+dfsg-2+b1 Source Version: 2.4.0+dfsg-2 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/debrebuildUgmYZz/debrebuild.tar.wTud8jq0Ip3B to /srv/rebuilderd/tmp/tmp.sbuild.vuPCHq2c7N... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Tue, 21 Jul 2026 11:02:42 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 21 Jul 2026 11:02:44 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-ntYJ50/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Tue, 21 Jul 2026 11:02:47 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64) +------------------------------------------------------------------------------+ | Build environment Tue, 21 Jul 2026 11:02:47 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.95+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.95-1 (2026-07-04) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-2 build-essential_12.12 bzip2_1.0.8-6+b2 chrpath_0.18-1 cmake_4.3.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.17-1 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gfortran-15_15.3.0-1 gfortran-15-x86-64-linux-gnu_15.3.0-1 googletest_1.17.0-1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_63.0-2 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.8-2 libasan8_16.1.0-2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-2 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-3 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-2 libclang-common-21-dev_1:21.1.8-7+b4 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl4t64_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-3 libdrm-common_2.4.134-3 libdrm2_2.4.134-3 libedit2_3.1-20260512-1 libeigen3-dev_3.4.0-5 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.13-stable-1 libevent-core-2.1-7t64_2.1.13-stable-1 libevent-dev_2.1.13-stable-1 libevent-extra-2.1-7t64_2.1.13-stable-1 libevent-openssl-2.1-7t64_2.1.13-stable-1 libevent-pthreads-2.1-7t64_2.1.13-stable-1 libexpat1_2.8.2-1 libfabric1_2.1.0-1.1+b2 libffi8_3.7.1-2 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.3.0-1 libgfortran5_16.1.0-2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgomp1_16.1.0-2 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-2 libhwloc-dev_2.14.0-2 libhwloc-plugins_2.14.0-2 libhwloc15_2.14.0-2 libibmad5_63.0-2 libibumad3_63.0-2 libibverbs-dev_63.0-2 libibverbs1_63.0-2 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp26_1.9.8-2 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 libldap2_2.6.13+dfsg-1 libllvm21_1:21.1.8-7+b4 liblocale-gettext-perl_1.07-10 liblsan0_16.1.0-2 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-2 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpciaccess0_0.19-2 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3+b2 libproc2-1_2:4.0.6-2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.23.0-1 libpsm2-2_11.2.185-2.1 libquadmath0_16.1.0-2 librdmacm1t64_63.0-2 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsframe3_2.46.50.20260617-1 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.2-2 libsprng2_2.0a-19 libsprng2-dev_2.0a-19 libssh2-1t64_1.11.1-4 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd-shared_261.1-3 libsystemd0_261.1-3 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libucc1_1.8.0-2 libuchardet0_0.0.8-2+b2 libucx0_1.22.0~rc1-1 libudev1_261.1-3 libunistring5_1.4.2-1 libuuid1_2.42.2-2 libuv1t64_1.52.1-4 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.3+dfsg-1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libyaml-cpp-dev_0.9.0+dfsg-5 libyaml-cpp0.9_0.9.0+dfsg-5 libz3-4_4.13.3-1.1 libze1_1.28.2-2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mpi-default-dev_1.20 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.4p1-1 openssh-common_1:10.4p1-1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 pci.ids_0.0~2026.07.06-1 perl_5.40.1-8 perl-base_5.40.1-8 perl-modules-5.40_5.40.1-8 pkg-config_2.5.1-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 procps_2:4.0.6-2 rpcsvc-proto_1.4.4-1 sed_4.9-3 sensible-utils_0.0.26 systemd_261.1-3 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 time_1.10-0.1 util-linux_2.42.2-2 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Tue, 21 Jul 2026 11:02:47 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree Binary: iqtree Architecture: amd64 Version: 2.4.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Kevin Murray Homepage: http://www.iqtree.org/ Standards-Version: 4.7.4 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, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree deb science optional arch=amd64 Checksums-Sha1: 56cdc0e17b6567b9d929dff852a4882ce99ac13b 2291260 iqtree_2.4.0+dfsg.orig.tar.xz 16e657ac5b3796234d4ab215c7673d73308c6c9c 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz Checksums-Sha256: cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e 2291260 iqtree_2.4.0+dfsg.orig.tar.xz b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz Files: 59ee0f3268c48e3654b0113bde82d8ff 2291260 iqtree_2.4.0+dfsg.orig.tar.xz b273612f949e5447f93f2e5e7f94d0c3 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmooKPERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGerQ/+K/afBBTQUj9D0tUgWufuEgBpyB6CJ4eL LiQ80yLgL3MseEwKqnmWSN410pxiSCWwvajSPLRIg8TjpEhkfCRYlSgk9QANSo6f xAJLYIYFS5wfbbsi6mB8lo36EIqtqHrVvESU+ay3LfPeEo0mTRHr8bgDhzc0M9sB vPSHegZyTRMjSYijk7f6cgHpMSOtRfLlg+KdEjEOzyIYVTfIJE0MRj9/39N0Ke8m rwOv6JCD/7nDi/YrEJqAazXTvLKEvdrCxn4PH/dKQ39zTNaCOnyrzvxyS9zSkiG1 9KLxsFYqK4bLSKdJDzeaTbGu61vDFg/Xe/ztOrOTxyUt41NMeGUChl3eBGaLBElA 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iqtree_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.4.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-libs dpkg-source: info: applying cmake-4.patch dpkg-source: info: applying libeigen5.0.patch Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 2.4.0+dfsg-2+b1 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=1784059727 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.4.0+dfsg-2+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-grnet-03) 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-2.4.0+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-2.4.0+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-2.4.0+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-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_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - 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/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (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-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : omp Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.3.0 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 unistd.h -- Looking for unistd.h - 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 "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.4s) CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-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_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - 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/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (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-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.3.0 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 unistd.h -- Looking for unistd.h - 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 "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.4s) CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-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_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - 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/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (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-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : mpi Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.3.0 Target binary : 64-bit -- 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") 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 unistd.h -- Looking for unistd.h - 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 "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (2.1s) CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at phylo-yaml/CMakeLists.txt:6 (target_link_libraries): The library that is being linked to, yaml-cpp, is marked as being deprecated by the owner. The message provided by the developer is: The target yaml-cpp is deprecated and will be removed in version 0.10.0. Use the yaml-cpp::yaml-cpp target instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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 lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreeavx.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelfma.cpp [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/bitset_index.c [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelsse.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/sort.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+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 booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree.c [ 3%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/booster.c [ 4%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 4%] Built target pllavx make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/alignment.c [ 4%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashtables_bfields.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/prng.c [ 5%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/bipartitionList.c [ 6%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/stats.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree_utils.c [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 6%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/lexer.c [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 14%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/parsePartition.c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+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/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancedatum.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+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/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+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 CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancesblock.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+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/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/stack.c [ 18%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+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 CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsemptyblock.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+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 CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsexception.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsreader.cpp [ 21%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 21%] Built target pll [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsstring.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstoken.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/mpdablock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstreesblock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msetsblock.cpp [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 24%] Built target ncl make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/primes-lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 27%] Built target sprng [ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/modelsblock.cpp make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 29%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Built target lsd2 make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen.c [ 29%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Built target nclextra make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 30%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 30%] Built target vectorclass make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/binomial_tpe.cpp [ 30%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 30%] Built target lbfgsb make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 30%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/multinomial.cpp [ 31%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen_sym.c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/pow_int.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/random.c [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gauss.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda.c [ 32%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda_sub.c [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gaussinv.cpp [ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest.c [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gausspdf.cpp [ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 34%] Built target gsl [ 34%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 35%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp [ 37%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 37%] Linking CXX static library libkernelsse.a [ 37%] Built target whtest /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/advanced.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 37%] Built target kernelsse [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bigint.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bipartitions.cpp [ 38%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 38%] Built target cmaple_utils make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 42%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/eigendecomposition.cpp [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 43%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/constraints.cpp [ 43%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/gzstream.cpp [ 43%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 43%] Built target phyloYAML [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/errors.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree.cpp [ 45%] 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 [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 45%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/optimization.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 45%] Built target kernelfma [ 45%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/nodes.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/parser.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/stoprule.cpp [ 47%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 47%] 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/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 47%] Built target kernelavx [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 48%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/simple.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/circularnetwork.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/tools.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/pllnni.cpp make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 49%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/trees.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 50%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 [ 51%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/greedy.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 52%] Built target decentTree [ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/checkpoint.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg 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CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/validation.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 53%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 [ 53%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 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make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 53%] Built target terraphast [ 53%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 54%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/hashsplitset.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdnetwork.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pruning.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/split.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitgraph.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 58%] Built target cmaple_alignment make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitset.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pda/lpwrapper.c [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopd.cpp [ 62%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 62%] Built target utils [ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/graph.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtree.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtreeset.cpp make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmarkov.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 64%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 64%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 65%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp [ 65%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 65%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelbin.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modeldna.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp [ 66%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 66%] Built target pda [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactory.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelprotein.cpp [ 67%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 67%] Built target cmaple_tree [ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelset.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodel.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 68%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategamma.cpp [ 69%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 69%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategammainvar.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 70%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS 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CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateinvar.cpp [ 72%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratekategory.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefree.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefreeinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachy.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelcodon.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmorphology.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmixture.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelunrest.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomomixture.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 76%] Built target cmaple [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/modeldnaerror.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/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.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 CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.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 CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.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/genomenode.cpp.o CMakeFiles/tree.dir/genometree.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 CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -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-2.4.0+dfsg/terrace/terrace.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/main.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phyloanalysis.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phylotesting.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+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 simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a /usr/lib/x86_64-linux-gnu/libyaml-cpp.so.0.9.0 booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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 lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make 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-fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelsse.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelfma.cpp [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/bitset_index.c [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/sort.c [ 2%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/booster.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashtables_bfields.c [ 3%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/prng.c [ 4%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/stats.c [ 5%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 5%] Built target pllavx make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 5%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 5%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree_utils.c [ 6%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/bipartitionList.c [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 6%] Built target booster [ 7%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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 C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/makenewzGenericSpecial.c [ 9%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/queue.c [ 13%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/restartHashTable.c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+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/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/ssort.c [ 14%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/stack.c [ 15%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+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/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+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/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+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/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 16%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 16%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 16%] Built target pll make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 17%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/mpdablock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsblock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msetsblock.cpp [ 20%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/modelsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 22%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 22%] Built target nclextra make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 23%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/lcg64.c [ 23%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/makeseed.c [ 23%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/memory.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/store.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/primes-lcg64.c [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancedatum.cpp [ 24%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/checkid.c [ 25%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 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-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancesblock.cpp [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsemptyblock.cpp [ 27%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 27%] Built target lsd2 make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 27%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/circularnetwork.cpp [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsexception.cpp [ 27%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 27%] Built target lbfgsb [ 28%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/greedy.cpp [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsreader.cpp [ 29%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxssetreader.cpp [ 29%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/hashsplitset.cpp [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsstring.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen.c [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstaxablock.cpp [ 30%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdnetwork.cpp [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen_sym.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/random.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda_sub.c [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest.c [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstoken.cpp [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 33%] 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/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 33%] Built target kernelsse make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 33%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstreesblock.cpp [ 34%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 34%] Built target vectorclass [ 34%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pruning.cpp [ 35%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 35%] Built target whtest [ 35%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/split.cpp [ 36%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake [ 37%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitgraph.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Built target kernelfma make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/binomial_tpe.cpp [ 38%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/multinomial.cpp [ 38%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 38%] Built target ncl [ 38%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitset.cpp [ 38%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/pow_int.cpp [ 38%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pda/lpwrapper.c [ 40%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopd.cpp [ 40%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gauss.cpp make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 40%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp [ 41%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gaussinv.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 41%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gausspdf.cpp [ 41%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 41%] Built target gsl [ 41%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/graph.cpp [ 41%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtree.cpp [ 41%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp [ 41%] 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/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 41%] Built target kernelavx [ 42%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.serial' [ 43%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 44%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtreeset.cpp [ 44%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp [ 44%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Built target cmaple_utils [ 44%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopdmtreeset.cpp make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/advanced.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bigint.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bipartitions.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 47%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 47%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 47%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 47%] Built target pda [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 47%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 48%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/eigendecomposition.cpp make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 48%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 49%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/constraints.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp [ 51%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 51%] Built target phyloYAML [ 51%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/gzstream.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/errors.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/optimization.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/stoprule.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/nodes.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/parser.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/tools.cpp [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/simple.cpp [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/trees.cpp [ 57%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 57%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 57%] Linking CXX static library libcmaple_alignment.a [ 57%] Built target decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake [ 57%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/pllnni.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 57%] Built target cmaple_alignment [ 57%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/validation.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/checkpoint.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 60%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 60%] Built target terraphast [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/MPIHelper.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 61%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 62%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 62%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 63%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 63%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 64%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 65%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelbin.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modeldna.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactory.cpp [ 67%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 67%] Built target cmaple_tree [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelprotein.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelset.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 68%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodel.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategamma.cpp [ 69%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 69%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 71%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratekategory.cpp [ 73%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefree.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefreeinvar.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachy.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelcodon.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmorphology.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 75%] Built target cmaple [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelunrest.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomomixture.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/modeldnaerror.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/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.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 CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/pattern.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.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 CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/iqtree.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/candidateset.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.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/genomenode.cpp.o CMakeFiles/tree.dir/genometree.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 CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE 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/build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -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-2.4.0+dfsg/terrace/terrace.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/main.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phyloanalysis.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/timetree.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+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 simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a /usr/lib/x86_64-linux-gnu/libyaml-cpp.so.0.9.0 booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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 lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreeavx.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/bitset_index.c [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelfma.cpp [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylokernelsse.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/sort.c [ 2%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/booster.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/hashtables_bfields.c [ 3%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/prng.c [ 4%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 4%] Built target pllavx [ 5%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/stats.c [ 5%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/booster/tree_utils.c [ 6%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Built target booster make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+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 C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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 C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 7%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsblock.cpp [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+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); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+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/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+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/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+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/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/restartHashTable.c [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+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/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+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 CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/ssort.c [ 16%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/stack.c [ 17%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/topologies.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+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/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+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/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsemptyblock.cpp [ 20%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 20%] Built target pll make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 21%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/mpdablock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsexception.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsreader.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msetsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxssetreader.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxsstring.cpp [ 23%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstaxablock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/nclextra/modelsblock.cpp [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstoken.cpp [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/ncl/nxstreesblock.cpp [ 25%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 25%] Built target nclextra make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 26%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/makeseed.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/memory.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/store.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/primes-lcg64.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/sprng/checkid.c [ 28%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 28%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 29%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/circularnetwork.cpp [ 29%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Built target lbfgsb [ 30%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/greedy.cpp [ 30%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 30%] Built target lsd2 make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/eigen_sym.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/random.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 31%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/weisslambda_sub.c [ 31%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 32%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest.c /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 33%] Built target vectorclass [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+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-2.4.0+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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/binomial_tpe.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/multinomial.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/pow_int.cpp [ 34%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gauss.cpp [ 34%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/hashsplitset.cpp [ 35%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gaussinv.cpp [ 35%] 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/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] Built target kernelsse make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp [ 35%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/gsl/gausspdf.cpp [ 35%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] Built target gsl [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp [ 37%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdnetwork.cpp [ 38%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 38%] Built target whtest [ 38%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp [ 38%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pruning.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.mpi' [ 40%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 40%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 40%] Built target cmaple_utils make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/advanced.cpp [ 40%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/split.cpp [ 41%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitgraph.cpp [ 42%] 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 /usr/bin/x86_64-linux-gnu-ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 42%] Built target kernelfma [ 42%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/splitset.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bigint.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bipartitions.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 44%] 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 [ 44%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake [ 44%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -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-2.4.0+dfsg/pda/lpwrapper.c cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 45%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o [ 45%] Built target kernelavx cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 46%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopd.cpp /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 46%] Built target phyloYAML [ 46%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/graph.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp [ 47%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtree.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/pdtreeset.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/constraints.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 49%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/eigendecomposition.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/gzstream.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/errors.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree.cpp make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/optimization.cpp [ 50%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/nodes.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/stoprule.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/parser.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 53%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 54%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/tools.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/simple.cpp [ 54%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 55%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 55%] Built target pda [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp [ 56%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 56%] Built target decentTree [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/trees.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/pllnni.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/checkpoint.cpp [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -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-2.4.0+dfsg/terraphast/lib/validation.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake [ 58%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/utils/MPIHelper.cpp "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 58%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 [ 60%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp /usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 60%] Built target terraphast make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 61%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 62%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 63%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 63%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 63%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 64%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 65%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modeldna.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelbin.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactory.cpp [ 67%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelprotein.cpp [ 67%] Built target cmaple_tree [ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelset.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 68%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodel.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 69%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rategammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 71%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratekategory.cpp [ 73%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefree.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/ratefreeinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachy.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelcodon.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmorphology.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelmixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelunrest.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Built target cmaple [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelpomomixture.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/modeldnaerror.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/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.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 CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.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 CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/iqtree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.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/genomenode.cpp.o CMakeFiles/tree.dir/genometree.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 CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -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-2.4.0+dfsg/terrace/terrace.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/main.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/treetesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/phyloanalysis.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-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 CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+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 simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a /usr/lib/x86_64-linux-gnu/libyaml-cpp.so.0.9.0 booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp ... + time /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Jul 14 2026 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy Seed: 9630 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Jul 21 11:15:05 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 Analyzing sequences: done in 3.51651e-05 secs using 99.53% CPU 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: -11281.626 Optimal log-likelihood: -11281.406 Rate parameters: A-C: 1.50410 A-G: 2.41208 A-T: 1.88844 C-G: 2.06994 C-T: 2.87791 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.088 Gamma shape alpha: 1.658 Parameters optimization took 1 rounds (0.034 sec) Time for fast ML tree search: 0.195 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 384 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11809.228 93 23804.457 23864.746 24171.866 2 GTR+F+I 11568.500 94 23325.000 23386.799 23696.360 3 GTR+F+G4 11300.280 94 22788.560 22850.359 23159.921 4 GTR+F+I+G4 11281.420 95 22752.841 22816.174 23128.152 5 GTR+F+R2 11394.985 95 22979.969 23043.303 23355.280 6 GTR+F+R3 11279.771 97 22753.542 22820.018 23136.755 7 GTR+F+R4 11273.337 99 22744.673 22814.392 23135.787 8 GTR+F+R5 11273.240 101 22748.481 22821.544 23147.495 14 GTR+F+I+R2 11314.078 96 22820.155 22885.047 23199.417 15 GTR+F+I+R3 11276.543 98 22749.086 22817.170 23136.249 16 GTR+F+I+R4 11271.314 100 22742.628 22814.006 23137.692 26 SYM+I+G4 11284.268 92 22752.536 22811.340 23115.995 28 SYM+R3 11281.135 94 22750.270 22812.069 23121.630 29 SYM+R4 11275.869 96 22743.738 22808.629 23122.999 37 SYM+I+R3 11278.351 95 22746.703 22810.036 23122.014 38 SYM+I+R4 11273.982 97 22741.964 22808.439 23125.176 48 TVM+F+I+G4 11283.811 94 22755.622 22817.422 23126.983 50 TVM+F+R3 11283.893 96 22759.785 22824.677 23139.047 51 TVM+F+R4 11276.752 98 22749.504 22817.588 23136.667 59 TVM+F+I+R3 11280.373 97 22754.746 22821.222 23137.959 60 TVM+F+I+R4 11275.104 99 22748.208 22817.926 23139.322 70 TVMe+I+G4 11286.110 91 22754.221 22811.563 23113.729 72 TVMe+R3 11284.504 93 22755.009 22815.298 23122.418 73 TVMe+R4 11278.704 95 22747.409 22810.742 23122.720 81 TVMe+I+R3 11281.535 94 22751.069 22812.868 23122.429 82 TVMe+I+R4 11277.123 96 22746.247 22811.139 23125.509 92 TIM3+F+I+G4 11300.535 93 22787.071 22847.361 23154.481 94 TIM3+F+R3 11298.969 95 22787.937 22851.270 23163.248 95 TIM3+F+R4 11291.420 97 22776.839 22843.315 23160.052 103 TIM3+F+I+R3 11295.702 96 22783.404 22848.296 23162.666 104 TIM3+F+I+R4 11289.455 98 22774.910 22842.994 23162.073 114 TIM3e+I+G4 11304.025 90 22788.049 22843.954 23143.607 116 TIM3e+R3 11300.928 92 22785.856 22844.660 23149.315 117 TIM3e+R4 11294.630 94 22777.260 22839.059 23148.620 125 TIM3e+I+R3 11298.155 93 22782.310 22842.599 23149.720 126 TIM3e+I+R4 11292.800 95 22775.599 22838.933 23150.910 136 TIM2+F+I+G4 11304.662 93 22795.325 22855.615 23162.735 138 TIM2+F+R3 11305.012 95 22800.025 22863.358 23175.336 139 TIM2+F+R4 11296.119 97 22786.238 22852.713 23169.450 147 TIM2+F+I+R3 11301.063 96 22794.126 22859.018 23173.388 148 TIM2+F+I+R4 11293.986 98 22783.973 22852.057 23171.136 158 TIM2e+I+G4 11312.332 90 22804.665 22860.569 23160.223 160 TIM2e+R3 11311.800 92 22807.600 22866.404 23171.059 161 TIM2e+R4 11303.817 94 22795.634 22857.433 23166.994 169 TIM2e+I+R3 11308.167 93 22802.335 22862.625 23169.745 170 TIM2e+I+R4 11301.782 95 22793.564 22856.897 23168.875 180 TIM+F+I+G4 11287.796 93 22761.591 22821.881 23129.001 182 TIM+F+R3 11287.548 95 22765.097 22828.430 23140.408 183 TIM+F+R4 11279.400 97 22752.800 22819.276 23136.012 191 TIM+F+I+R3 11283.744 96 22759.489 22824.381 23138.751 192 TIM+F+I+R4 11277.275 98 22750.550 22818.634 23137.713 202 TIMe+I+G4 11294.556 90 22769.111 22825.016 23124.669 204 TIMe+R3 11293.653 92 22771.305 22830.109 23134.764 205 TIMe+R4 11286.378 94 22760.756 22822.555 23132.116 213 TIMe+I+R3 11290.093 93 22766.185 22826.475 23133.595 214 TIMe+I+R4 11284.336 95 22758.672 22822.005 23133.983 224 TPM3u+F+I+G4 11302.964 92 22789.928 22848.732 23153.387 226 TPM3u+F+R3 11303.038 94 22794.076 22855.876 23165.437 227 TPM3u+F+R4 11295.084 96 22782.169 22847.061 23161.430 235 TPM3u+F+I+R3 11299.544 95 22789.088 22852.421 23164.399 236 TPM3u+F+I+R4 11293.460 97 22780.921 22847.396 23164.133 246 TPM3+I+G4 11305.851 89 22789.701 22844.191 23141.308 248 TPM3+R3 11304.230 91 22790.460 22847.802 23149.968 249 TPM3+R4 11297.667 93 22781.335 22841.625 23148.745 257 TPM3+I+R3 11301.287 92 22786.574 22845.378 23150.033 258 TPM3+I+R4 11296.105 94 22780.210 22842.009 23151.571 268 TPM2u+F+I+G4 11307.001 92 22798.002 22856.806 23161.461 270 TPM2u+F+R3 11309.018 94 22806.035 22867.835 23177.396 271 TPM2u+F+R4 11299.632 96 22791.264 22856.156 23170.526 279 TPM2u+F+I+R3 11304.766 95 22799.531 22862.864 23174.842 280 TPM2u+F+I+R4 11297.916 97 22789.832 22856.307 23173.044 290 TPM2+I+G4 11313.977 89 22805.953 22860.443 23157.561 292 TPM2+R3 11314.938 91 22811.877 22869.219 23171.385 293 TPM2+R4 11306.482 93 22798.963 22859.253 23166.373 301 TPM2+I+R3 11311.057 92 22806.114 22864.918 23169.573 302 TPM2+I+R4 11304.811 94 22797.622 22859.421 23168.982 312 K3Pu+F+I+G4 11290.121 92 22764.242 22823.047 23127.702 314 K3Pu+F+R3 11291.617 94 22771.234 22833.033 23142.594 315 K3Pu+F+R4 11282.773 96 22757.547 22822.439 23136.808 323 K3Pu+F+I+R3 11287.583 95 22765.165 22828.499 23140.476 324 K3Pu+F+I+R4 11281.086 97 22756.172 22822.648 23139.385 334 K3P+I+G4 11296.201 89 22770.401 22824.891 23122.009 336 K3P+R3 11296.854 91 22775.708 22833.051 23135.217 337 K3P+R4 11288.937 93 22763.874 22824.164 23131.284 345 K3P+I+R3 11293.092 92 22770.183 22828.987 23133.642 346 K3P+I+R4 11287.274 94 22762.547 22824.347 23133.908 356 TN+F+I+G4 11304.824 92 22793.648 22852.452 23157.107 358 TN+F+R3 11305.025 94 22798.049 22859.849 23169.410 359 TN+F+R4 11296.214 96 22784.428 22849.320 23163.690 367 TN+F+I+R3 11301.112 95 22792.223 22855.556 23167.534 368 TN+F+I+R4 11294.072 97 22782.145 22848.620 23165.357 378 TNe+I+G4 11312.397 89 22802.794 22857.284 23154.401 380 TNe+R3 11311.801 91 22805.602 22862.944 23165.110 381 TNe+R4 11303.889 93 22793.777 22854.067 23161.187 389 TNe+I+R3 11308.177 92 22800.355 22859.159 23163.814 390 TNe+I+R4 11301.844 94 22791.689 22853.488 23163.049 400 HKY+F+I+G4 11307.175 91 22796.351 22853.693 23155.859 402 HKY+F+R3 11309.040 93 22804.079 22864.369 23171.489 403 HKY+F+R4 11299.610 95 22789.220 22852.553 23164.531 411 HKY+F+I+R3 11304.838 94 22797.677 22859.476 23169.037 412 HKY+F+I+R4 11297.909 96 22787.819 22852.710 23167.080 422 K2P+I+G4 11314.049 88 22804.097 22857.195 23151.754 424 K2P+R3 11314.939 90 22809.879 22865.783 23165.437 425 K2P+R4 11306.474 92 22796.949 22855.753 23160.408 433 K2P+I+R3 11311.073 91 22804.147 22861.489 23163.655 434 K2P+I+R4 11304.807 93 22795.614 22855.904 23163.024 444 F81+F+I+G4 11352.324 90 22884.649 22940.553 23240.207 446 F81+F+R3 11353.480 92 22890.960 22949.764 23254.419 447 F81+F+R4 11344.938 94 22877.875 22939.675 23249.236 455 F81+F+I+R3 11349.527 93 22885.054 22945.343 23252.464 456 F81+F+I+R4 11343.197 95 22876.395 22939.728 23251.706 466 JC+I+G4 11356.715 87 22887.430 22939.160 23231.136 468 JC+R3 11357.017 89 22892.034 22946.524 23243.641 469 JC+R4 11349.374 91 22880.748 22938.091 23240.257 477 JC+I+R3 11353.328 90 22886.655 22942.559 23242.213 478 JC+I+R4 11347.659 92 22879.317 22938.121 23242.776 Akaike Information Criterion: SYM+I+R4 Corrected Akaike Information Criterion: SYM+I+R4 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: 8.403 seconds (0h:0m:8s) Wall-clock time for ModelFinder: 8.473 seconds (0h:0m:8s) 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, 1.667 / Estimate: 0.000, 0.981 / LogL: -11303.942 Init pinv, alpha: 0.012, 1.667 / Estimate: 0.087, 1.695 / LogL: -11286.100 Init pinv, alpha: 0.023, 1.667 / Estimate: 0.087, 1.695 / LogL: -11286.103 Init pinv, alpha: 0.035, 1.667 / Estimate: 0.087, 1.694 / LogL: -11286.108 Init pinv, alpha: 0.046, 1.667 / Estimate: 0.086, 1.692 / LogL: -11286.100 Init pinv, alpha: 0.058, 1.667 / Estimate: 0.087, 1.695 / LogL: -11286.100 Init pinv, alpha: 0.069, 1.667 / Estimate: 0.087, 1.697 / LogL: -11286.099 Init pinv, alpha: 0.081, 1.667 / Estimate: 0.087, 1.700 / LogL: -11286.099 Init pinv, alpha: 0.093, 1.667 / Estimate: 0.087, 1.700 / LogL: -11286.100 Init pinv, alpha: 0.104, 1.667 / Estimate: 0.087, 1.701 / LogL: -11286.099 Optimal pinv,alpha: 0.087, 1.701 / LogL: -11286.099 Parameters optimization took 1.006 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00828347 secs using 99.86% CPU Computing ML distances took 0.008433 sec (of wall-clock time) 0.008382 sec (of CPU time) Setting up auxiliary I and S matrices: done in 9.37581e-05 secs using 100.3% CPU Computing RapidNJ tree took 0.000388 sec (of wall-clock time) 0.000318 sec (of CPU time) Log-likelihood of RapidNJ tree: -11282.322 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.350 second Computing log-likelihood of 98 initial trees ... 0.424 seconds Current best score: -11265.288 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11231.066 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.172 Iteration 10 / LogL: -11226.947 / Time: 0h:0m:10s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 16: -11224.924 Iteration 20 / LogL: -11232.980 / Time: 0h:0m:11s Finish initializing candidate tree set (13) Current best tree score: -11224.924 / CPU time: 2.103 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11225.600 / Time: 0h:0m:12s (0h:0m:12s left) BETTER TREE FOUND at iteration 40: -11224.923 Iteration 40 / LogL: -11224.923 / Time: 0h:0m:13s (0h:0m:12s left) Iteration 50 / LogL: -11231.883 / Time: 0h:0m:14s (0h:0m:10s left) UPDATE BEST LOG-LIKELIHOOD: -11224.918 Iteration 60 / LogL: -11225.414 / Time: 0h:0m:15s (0h:0m:9s left) Iteration 70 / LogL: -11224.989 / Time: 0h:0m:16s (0h:0m:7s left) Iteration 80 / LogL: -11232.164 / Time: 0h:0m:16s (0h:0m:6s left) Estimate model parameters (epsilon = 0.100) UPDATE BEST LOG-LIKELIHOOD: -11224.876 Iteration 90 / LogL: -11228.816 / Time: 0h:0m:17s (0h:0m:5s left) Iteration 100 / LogL: -11224.936 / Time: 0h:0m:18s (0h:0m:4s left) Iteration 110 / LogL: -11225.148 / Time: 0h:0m:19s (0h:0m:3s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 113: -11224.387 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 115: -11224.096 Iteration 120 / LogL: -11224.176 / Time: 0h:0m:20s (0h:0m:9s left) Iteration 130 / LogL: -11224.505 / Time: 0h:0m:21s (0h:0m:8s left) UPDATE BEST LOG-LIKELIHOOD: -11224.096 Estimate model parameters (epsilon = 0.100) UPDATE BEST LOG-LIKELIHOOD: -11224.070 Iteration 140 / LogL: -11224.246 / Time: 0h:0m:21s (0h:0m:7s left) Iteration 150 / LogL: -11224.483 / Time: 0h:0m:22s (0h:0m:6s left) Iteration 160 / LogL: -11224.107 / Time: 0h:0m:23s (0h:0m:5s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 169: -11223.149 Iteration 170 / LogL: -11224.421 / Time: 0h:0m:24s (0h:0m:9s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 172: -11222.779 Iteration 180 / LogL: -11223.071 / Time: 0h:0m:25s (0h:0m:8s left) Iteration 190 / LogL: -11222.867 / Time: 0h:0m:26s (0h:0m:7s left) Iteration 200 / LogL: -11222.780 / Time: 0h:0m:26s (0h:0m:6s left) Iteration 210 / LogL: -11224.133 / Time: 0h:0m:27s (0h:0m:5s left) Iteration 220 / LogL: -11222.948 / Time: 0h:0m:28s (0h:0m:4s left) Iteration 230 / LogL: -11223.084 / Time: 0h:0m:29s (0h:0m:3s left) Iteration 240 / LogL: -11222.784 / Time: 0h:0m:30s (0h:0m:2s left) Iteration 250 / LogL: -11225.473 / Time: 0h:0m:31s (0h:0m:1s left) Iteration 260 / LogL: -11223.073 / Time: 0h:0m:31s (0h:0m:1s left) Iteration 270 / LogL: -11223.441 / Time: 0h:0m:32s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 273 ITERATIONS / Time: 0h:0m:32s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.779 Optimal log-likelihood: -11222.777 Rate parameters: A-C: 1.53079 A-G: 2.64069 A-T: 1.69353 C-G: 2.00528 C-T: 2.64069 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 (0.015 sec) BEST SCORE FOUND : -11222.777 Total tree length: 12.602 Total number of iterations: 273 CPU time used for tree search: 22.884 sec (0h:0m:22s) Wall-clock time used for tree search: 23.392 sec (0h:0m:23s) Total CPU time used: 32.345 sec (0h:0m:32s) Total wall-clock time used: 32.929 sec (0h:0m:32s) 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: Tue Jul 21 11:15:37 2026 32.35user 0.52system 0:32.93elapsed 99%CPU (0avgtext+0avgdata 17288maxresident)k 0inputs+344outputs (0major+4182minor)pagefaults 0swaps + time /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Jul 14 2026 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo Seed: 950995 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Jul 21 11:15:37 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 Analyzing sequences: done in 4.22909e-05 secs using 96.95% CPU 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)... 0.005 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: -11221.074 Rate parameters: A-C: 1.44162 A-G: 2.32359 A-T: 1.71208 C-G: 1.87669 C-T: 2.81396 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: 1.498 Parameters optimization took 1 rounds (0.017 sec) Time for fast ML tree search: 0.219 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 384 epsilon: 0.100) ... 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 22721.000 23030.561 4 GTR+F+I+G4 11221.091 95 22632.182 22695.516 23007.493 5 GTR+F+R2 11334.881 95 22859.762 22923.096 23235.073 6 GTR+F+R3 11221.214 97 22636.427 22702.903 23019.640 7 GTR+F+R4 11214.955 99 22627.910 22697.628 23019.024 8 GTR+F+R5 11214.756 101 22631.512 22704.575 23030.527 14 GTR+F+I+R2 11262.734 96 22717.468 22782.360 23096.730 15 GTR+F+I+R3 11217.321 98 22630.641 22698.725 23017.804 16 GTR+F+I+R4 11213.562 100 22627.124 22698.502 23022.188 26 SYM+I+G4 11224.587 92 22633.174 22691.978 22996.633 48 TVM+F+I+G4 11223.880 94 22635.760 22697.560 23007.121 70 TVMe+I+G4 11226.720 91 22635.439 22692.782 22994.948 92 TIM3+F+I+G4 11234.231 93 22654.462 22714.752 23021.872 114 TIM3e+I+G4 11238.336 90 22656.671 22712.576 23012.229 136 TIM2+F+I+G4 11237.940 93 22661.880 22722.170 23029.290 158 TIM2e+I+G4 11246.028 90 22672.056 22727.960 23027.613 180 TIM+F+I+G4 11226.692 93 22639.384 22699.674 23006.794 202 TIMe+I+G4 11233.949 90 22647.898 22703.803 23003.456 224 TPM3u+F+I+G4 11237.183 92 22658.365 22717.169 23021.824 246 TPM3+I+G4 11240.569 89 22659.138 22713.628 23010.745 268 TPM2u+F+I+G4 11240.786 92 22665.571 22724.376 23029.031 290 TPM2+I+G4 11248.069 89 22674.138 22728.627 23025.745 312 K3Pu+F+I+G4 11229.446 92 22642.893 22701.697 23006.352 334 K3P+I+G4 11235.913 89 22649.827 22704.317 23001.434 356 TN+F+I+G4 11238.124 92 22660.248 22719.052 23023.707 378 TNe+I+G4 11246.111 89 22670.222 22724.712 23021.829 400 HKY+F+I+G4 11240.988 91 22663.975 22721.317 23023.483 422 K2P+I+G4 11248.161 88 22672.323 22725.421 23019.979 444 F81+F+I+G4 11292.697 90 22765.394 22821.298 23120.952 466 JC+I+G4 11297.067 87 22768.134 22819.864 23111.840 Akaike Information Criterion: GTR+F+I+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: 2.754 seconds (0h:0m:2s) Wall-clock time for ModelFinder: 2.777 seconds (0h:0m:2s) 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, 1.517 / Estimate: 0.000, 0.943 / LogL: -11240.359 Init pinv, alpha: 0.012, 1.517 / Estimate: 0.083, 1.533 / LogL: -11226.719 Init pinv, alpha: 0.023, 1.517 / Estimate: 0.083, 1.531 / LogL: -11226.723 Init pinv, alpha: 0.035, 1.517 / Estimate: 0.083, 1.529 / LogL: -11226.723 Init pinv, alpha: 0.046, 1.517 / Estimate: 0.083, 1.536 / LogL: -11226.717 Init pinv, alpha: 0.058, 1.517 / Estimate: 0.083, 1.532 / LogL: -11226.718 Init pinv, alpha: 0.069, 1.517 / Estimate: 0.083, 1.538 / LogL: -11226.717 Init pinv, alpha: 0.081, 1.517 / Estimate: 0.084, 1.542 / LogL: -11226.716 Init pinv, alpha: 0.093, 1.517 / Estimate: 0.084, 1.543 / LogL: -11226.715 Init pinv, alpha: 0.104, 1.517 / Estimate: 0.084, 1.545 / LogL: -11226.718 Optimal pinv,alpha: 0.084, 1.543 / LogL: -11226.715 Parameters optimization took 1.050 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00863987 secs using 99.52% CPU Computing ML distances took 0.008815 sec (of wall-clock time) 0.008728 sec (of CPU time) Setting up auxiliary I and S matrices: done in 7.8005e-05 secs using 98.71% CPU Computing RapidNJ tree took 0.000364 sec (of wall-clock time) 0.000295 sec (of CPU time) Log-likelihood of RapidNJ tree: -11281.910 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.348 second Computing log-likelihood of 98 initial trees ... 0.431 seconds Current best score: -11226.715 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.742 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.128 Iteration 10 / LogL: -11227.720 / Time: 0h:0m:5s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 18: -11224.931 Iteration 20 / LogL: -11226.359 / Time: 0h:0m:5s Finish initializing candidate tree set (17) Current best tree score: -11224.931 / CPU time: 2.122 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11225.812 / Time: 0h:0m:6s (0h:0m:12s left) Iteration 40 / LogL: -11225.645 / Time: 0h:0m:7s (0h:0m:9s left) Iteration 50 / LogL: -11225.200 / Time: 0h:0m:8s (0h:0m:7s left) Iteration 60 / LogL: -11225.447 / Time: 0h:0m:9s (0h:0m:6s left) Iteration 70 / LogL: -11225.773 / Time: 0h:0m:10s (0h:0m:5s left) Iteration 80 / LogL: -11225.120 / Time: 0h:0m:10s (0h:0m:3s left) UPDATE BEST LOG-LIKELIHOOD: -11224.930 Iteration 90 / LogL: -11224.930 / Time: 0h:0m:11s (0h:0m:2s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 97: -11224.732 Iteration 100 / LogL: -11225.013 / Time: 0h:0m:12s (0h:0m:9s left) Iteration 110 / LogL: -11227.181 / Time: 0h:0m:13s (0h:0m:8s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 113: -11224.098 Iteration 120 / LogL: -11225.051 / Time: 0h:0m:14s (0h:0m:8s left) BETTER TREE FOUND at iteration 122: -11224.092 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 123: -11222.782 Iteration 130 / LogL: -11224.435 / Time: 0h:0m:15s (0h:0m:8s left) Iteration 140 / LogL: -11222.920 / Time: 0h:0m:15s (0h:0m:7s left) Iteration 150 / LogL: -11223.719 / Time: 0h:0m:16s (0h:0m:6s left) UPDATE BEST LOG-LIKELIHOOD: -11222.782 Iteration 160 / LogL: -11226.948 / Time: 0h:0m:17s (0h:0m:5s left) Iteration 170 / LogL: -11223.209 / Time: 0h:0m:18s (0h:0m:4s left) Iteration 180 / LogL: -11231.630 / Time: 0h:0m:19s (0h:0m:3s left) Iteration 190 / LogL: -11234.929 / Time: 0h:0m:20s (0h:0m:3s left) Iteration 200 / LogL: -11223.052 / Time: 0h:0m:20s (0h:0m:2s left) Iteration 210 / LogL: -11223.441 / Time: 0h:0m:21s (0h:0m:1s left) Iteration 220 / LogL: -11222.983 / Time: 0h:0m:22s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 224 ITERATIONS / Time: 0h:0m:22s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.782 Optimal log-likelihood: -11222.777 Rate parameters: A-C: 1.50492 A-G: 2.58833 A-T: 1.65800 C-G: 1.96397 C-T: 2.58833 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 (0.016 sec) BEST SCORE FOUND : -11222.777 Total tree length: 12.606 Total number of iterations: 224 CPU time used for tree search: 18.587 sec (0h:0m:18s) Wall-clock time used for tree search: 18.972 sec (0h:0m:18s) Total CPU time used: 22.441 sec (0h:0m:22s) Total wall-clock time used: 22.857 sec (0h:0m:22s) 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: Tue Jul 21 11:16:00 2026 22.45user 0.39system 0:22.86elapsed 99%CPU (0avgtext+0avgdata 17200maxresident)k 0inputs+280outputs (0major+5728minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.TaZ4yC 54.82user 0.93system 0:55.85elapsed 99%CPU (0avgtext+0avgdata 17288maxresident)k 0inputs+672outputs (0major+11633minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j6 install DESTDIR=/build/reproducible-path/iqtree-2.4.0\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+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-2.4.0+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' mkdir -p /build/reproducible-path/iqtree-2.4.0+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="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/reproducible-path/iqtree-2.4.0+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="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/reproducible-path/iqtree-2.4.0+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="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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' in '../iqtree_2.4.0+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree_2.4.0+dfsg-2+b1_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 2026-07-21T11:17:49Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 21 Jul 2026 11:17:49 +0000 | +------------------------------------------------------------------------------+ iqtree_2.4.0+dfsg-2+b1_amd64.changes: ------------------------------------- Format: 1.8 Date: Tue, 14 Jul 2026 20:08:47 +0000 Source: iqtree (2.4.0+dfsg-2) Binary: iqtree iqtree-dbgsym Binary-Only: yes Architecture: amd64 Version: 2.4.0+dfsg-2+b1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: all / amd64 / i386 Build Daemon (x86-grnet-03) Description: iqtree - efficient phylogenetic software by maximum likelihood Changes: iqtree (2.4.0+dfsg-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 Checksums-Sha1: 4d02c5154153445a180e5185f812859d8cf29572 115207204 iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb af0cf9d559514e137aa506aff18fb23afbd129fc 8855 iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo 6a786be8f601146c84f0c3a2e094eda5d41b9e46 10310440 iqtree_2.4.0+dfsg-2+b1_amd64.deb Checksums-Sha256: 4cce1bb21feb6aae3f7071962d943e6b5f7d18a3a41084bf8859ebb154fdd284 115207204 iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb 9cc99467b3a43099601c316622c7a4cdccbde89eba7ebec6e837bc8ea57e9e8a 8855 iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo eedbb4f217f7dd5762d370f8d2b4a68eadbd964764bf3d632a71f8e87d1bc666 10310440 iqtree_2.4.0+dfsg-2+b1_amd64.deb Files: 7ace5e61f6a366b2b1b1f8635ebd95e8 115207204 debug optional iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb dae2563fa34f232805f7508b9296caef 8855 science optional iqtree_2.4.0+dfsg-2+b1_amd64.buildinfo a1269914d168926b76a1094e3002b592 10310440 science optional iqtree_2.4.0+dfsg-2+b1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 21 Jul 2026 11:17:50 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree (2.4.0+dfsg-2) Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.4.0+dfsg-2+b1 Binary-Only-Changes: iqtree (2.4.0+dfsg-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 . -- all / amd64 / i386 Build Daemon (x86-grnet-03) Tue, 14 Jul 2026 20:08:47 +0000 Checksums-Md5: 7ace5e61f6a366b2b1b1f8635ebd95e8 115207204 iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb a1269914d168926b76a1094e3002b592 10310440 iqtree_2.4.0+dfsg-2+b1_amd64.deb Checksums-Sha1: 4d02c5154153445a180e5185f812859d8cf29572 115207204 iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb 6a786be8f601146c84f0c3a2e094eda5d41b9e46 10310440 iqtree_2.4.0+dfsg-2+b1_amd64.deb Checksums-Sha256: 4cce1bb21feb6aae3f7071962d943e6b5f7d18a3a41084bf8859ebb154fdd284 115207204 iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb eedbb4f217f7dd5762d370f8d2b4a68eadbd964764bf3d632a71f8e87d1bc666 10310440 iqtree_2.4.0+dfsg-2+b1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 21 Jul 2026 11:17:47 +0000 Build-Path: /build/reproducible-path/iqtree-2.4.0+dfsg Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 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libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-2), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-ossl0 (= 1.22.1-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpciaccess0 (= 0.19-2), libpcre2-8-0 (= 10.46-1+b2), libperl5.40 (= 5.40.1-8), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 6.0.0+really5.0.9-3+b2), libproc2-1 (= 2:4.0.6-2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.23.0-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16.1.0-2), librdmacm1t64 (= 63.0-2), librhash1 (= 1.4.6-1.1+b1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.2-2), libsprng2 (= 2.0a-19), libsprng2-dev (= 2.0a-19), libssh2-1t64 (= 1.11.1-4), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd-shared (= 261.1-3), libsystemd0 (= 261.1-3), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libucc1 (= 1.8.0-2), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.22.0~rc1-1), libudev1 (= 261.1-3), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-2), libuv1t64 (= 1.52.1-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libxxhash0 (= 0.8.3-2+b2), libyaml-cpp-dev (= 0.9.0+dfsg-5), libyaml-cpp0.9 (= 0.9.0+dfsg-5), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.4p1-1), openssh-common (= 1:10.4p1-1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), pci.ids (= 0.0~2026.07.06-1), perl (= 5.40.1-8), perl-base (= 5.40.1-8), perl-modules-5.40 (= 5.40.1-8), pkg-config (= 2.5.1-4), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), procps (= 2:4.0.6-2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261.1-3), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.10-0.1), util-linux (= 2.42.2-2), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1784059727" +------------------------------------------------------------------------------+ | Package contents Tue, 21 Jul 2026 11:17:50 +0000 | +------------------------------------------------------------------------------+ iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb --------------------------------------- new Debian package, version 2.0. size 115207204 bytes: control archive=696 bytes. 482 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: iqtree-dbgsym Source: iqtree (2.4.0+dfsg-2) Version: 2.4.0+dfsg-2+b1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 122080 Depends: iqtree (= 2.4.0+dfsg-2+b1) Section: debug Priority: optional Description: debug symbols for iqtree Build-Ids: c349236d44aee8b04351df49b6f084ce35c75ca1 c613f438893d249a3102a077e308f118004f387b ce7f281c51b0a1b3f78ee44676b426e72c191386 drwxr-xr-x root/root 0 2026-07-14 20:08 ./ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.build-id/c3/ -rw-r--r-- root/root 36305048 2026-07-14 20:08 ./usr/lib/debug/.build-id/c3/49236d44aee8b04351df49b6f084ce35c75ca1.debug drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.build-id/c6/ -rw-r--r-- root/root 36213440 2026-07-14 20:08 ./usr/lib/debug/.build-id/c6/13f438893d249a3102a077e308f118004f387b.debug drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.build-id/ce/ -rw-r--r-- root/root 36213344 2026-07-14 20:08 ./usr/lib/debug/.build-id/ce/7f281c51b0a1b3f78ee44676b426e72c191386.debug drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 16261328 2026-07-14 20:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree.debug drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-07-14 20:08 ./usr/share/doc/iqtree-dbgsym -> iqtree iqtree_2.4.0+dfsg-2+b1_amd64.deb -------------------------------- new Debian package, version 2.0. size 10310440 bytes: control archive=1592 bytes. 1469 bytes, 30 lines control 1185 bytes, 17 lines md5sums Package: iqtree Source: iqtree (2.4.0+dfsg-2) Version: 2.4.0+dfsg-2+b1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 34667 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.9 (>= 0.7.0), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://www.iqtree.org/ 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 2026-07-14 20:08 ./ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/bin/ -rwxr-xr-x root/root 11012728 2026-07-14 20:08 ./usr/bin/iqtree2 -rwxr-xr-x root/root 11029112 2026-07-14 20:08 ./usr/bin/iqtree2-mpi -rwxr-xr-x root/root 11012728 2026-07-14 20:08 ./usr/bin/iqtree2-omp drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/doc/iqtree/ -rw-r--r-- root/root 278 2026-06-09 14:22 ./usr/share/doc/iqtree/README.test -rw-r--r-- root/root 235 2026-07-14 20:08 ./usr/share/doc/iqtree/changelog.Debian.amd64.gz -rw-r--r-- root/root 851 2026-07-14 20:08 ./usr/share/doc/iqtree/changelog.Debian.gz -rw-r--r-- root/root 8147 2026-06-09 14:22 ./usr/share/doc/iqtree/copyright drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/doc/iqtree/examples/ -rw-r--r-- root/root 939 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/custom_distributions.txt -rw-r--r-- root/root 2237314 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.cf -rw-r--r-- root/root 174 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.nex -rw-r--r-- root/root 34178 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.phy -rw-r--r-- root/root 121669 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/models.nex -rw-r--r-- root/root 47 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/tree.nwk -rw-r--r-- root/root 2188 2026-06-09 14:22 ./usr/share/doc/iqtree/run-unit-test drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/man/ drwxr-xr-x root/root 0 2026-07-14 20:08 ./usr/share/man/man1/ -rw-r--r-- root/root 6973 2026-07-14 20:08 ./usr/share/man/man1/iqtree2-mpi.1.gz -rw-r--r-- root/root 6971 2026-07-14 20:08 ./usr/share/man/man1/iqtree2-omp.1.gz -rw-r--r-- root/root 6953 2026-07-14 20:08 ./usr/share/man/man1/iqtree2.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 21 Jul 2026 11:17:52 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 21 Jul 2026 11:17:52 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 21 Jul 2026 11:17:54 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3337696 Build-Time: 901 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdbaEawj/inputs/iqtree_2.4.0+dfsg-2.dsc Machine Architecture: amd64 Package: iqtree Package-Time: 912 Source-Version: 2.4.0+dfsg-2 Space: 3337696 Status: successful Version: 2.4.0+dfsg-2+b1 -------------------------------------------------------------------------------- Finished at 2026-07-21T11:17:49Z Build needed 00:15:12, 3337696k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdbaEawj/out size differs for iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb checking iqtree-dbgsym_2.4.0+dfsg-2+b1_amd64.deb: