=============================================================================== 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/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+dfsg-2_amd64.buildinfo Source: iqtree3 Version: 3.1.1+dfsg-2 rebuilderd-worker node: osuosl41-amd64 +------------------------------------------------------------------------------+ | Downloading sources Fri, 12 Jun 2026 09:50:20 +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 [189 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 [176 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [86.0 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [263 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3,220 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8,528 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.9 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 [11.5 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [399 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 34.7 MB in 4s (9,237 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg-2.dsc' iqtree3_3.1.1+dfsg-2.dsc 2211 SHA256:414f97b0042b6fc76ee4a843a4ca4d00010eb5a2caddf56f25b00e045006bd8f 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg.orig.tar.xz' iqtree3_3.1.1+dfsg.orig.tar.xz 2314716 SHA256:abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg-2.debian.tar.xz' iqtree3_3.1.1+dfsg-2.debian.tar.xz 24212 SHA256:69c42c8624655fcbad54d233098f841c8f3bce130375c596d447f0a5b4356a13 abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 iqtree3_3.1.1+dfsg.orig.tar.xz 69c42c8624655fcbad54d233098f841c8f3bce130375c596d447f0a5b4356a13 iqtree3_3.1.1+dfsg-2.debian.tar.xz 414f97b0042b6fc76ee4a843a4ca4d00010eb5a2caddf56f25b00e045006bd8f iqtree3_3.1.1+dfsg-2.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Fri, 12 Jun 2026 09:50:24 +0000 | +------------------------------------------------------------------------------+ Rebuilding iqtree3=3.1.1+dfsg-2 in /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdzhXbrN/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+dfsg-2_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+dfsg-2_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/iqtree3-3.1.1+dfsg I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [189 kB] Get:2 http://snapshot.debian.org/archive/debian/20260611T143613Z forky InRelease [151 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.5 MB] Get:4 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 Packages [9760 kB] Fetched 20.6 MB in 2s (9479 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260611T143613Z/dists/forky/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprldkdsc4/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf7_xggpn/libjansson4_2.14-2+b4_amd64.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 (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp44w21isc/cpp_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.10-1 [85.4 kB] Fetched 85.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq8m6cfhq/libselinux1_3.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.3p1-4 [1003 kB] Fetched 1003 kB in 0s (69.5 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.3p1-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpchu955yt/openssh-client_10.3p1-4_amd64.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 (5435 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6o3o6vl4/base-passwd_3.6.8_amd64.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 (85.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbqlqdsv2/groff-base_1.24.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Fetched 61.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp13voy154/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 16.1.0-1 [27.0 kB] Fetched 27.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi29lstul/libitm1_16.1.0-1_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/tmpr3ql__g4/help2man_1.49.3_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/tmpvi8rk5kh/libxau6_1.0.11-1+b2_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/tmp4s7dgt1b/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.134-1 [21.5 kB] Fetched 21.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhcsgqj9/libdrm-radeon1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b2 [175 kB] Fetched 175 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkywh3ims/libpam-modules_1.7.0-5+b2_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/tmpgiuslao8/libzstd1_1.5.7+dfsg-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-16-base amd64 16.1.0-1 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkgllmxhx/gcc-16-base_16.1.0-1_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/tmpl2x4ep2l/libuchardet0_0.0.8-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-3 [244 kB] Fetched 244 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7c6927y_/libssh2-1t64_1.11.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16.1.0-1 [2888 kB] Fetched 2888 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbeobl12b/libasan8_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42.1-3 [213 kB] Fetched 213 kB in 0s (20.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqpjz0_2/libmount1_2.42.1-3_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 (67.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ponetdb/libze1_1.28.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.134-1 [64.1 kB] Fetched 64.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa9m1778e/libdrm-intel1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6+b2 [387 kB] Fetched 387 kB in 0s (1977 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwbmae2ts/libncl2_2.1.21+git20210811.b1213a7-6+b2_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/tmpudw5fp7o/libnghttp2-14_1.69.0-1_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 (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpgywjgxyq/gcc_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.26-1 [315 kB] Fetched 315 kB in 0s (24.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8yconrgd/gettext-base_0.26-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b2 [188 kB] Fetched 188 kB in 0s (17.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr949sqt5/libldap2_2.6.10+dfsg-1+b2_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/tmpkt910tyf/rpcsvc-proto_1.4.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 16.1.0-1 [823 kB] Fetched 823 kB in 0s (64.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpee08bna2/libstdc++6_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.7.0~rc1-1 [329 kB] Fetched 329 kB in 0s (30.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptjomd0vt/libucc1_1.7.0~rc1-1_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/tmptfa7hby9/libz3-4_4.13.3-1.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261~rc3-1 [2561 kB] Fetched 2561 kB in 0s (124 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgiv76pcd/libsystemd-shared_261~rc3-1_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 (84.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp16bi9w8p/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-1 [38.5 kB] Fetched 38.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr6xbyh5t/libdrm2_2.4.134-1_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/tmpmquf1fou/libsasl2-2_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b1 [28.2 MB] Fetched 28.2 MB in 0s (176 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpamse5l5y/libllvm21_21.1.8-7+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuwt3b001/libsprng2-dev_2.0a-19_amd64.deb' Get: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/tmpszx9vr7s/libcom-err2_1.47.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-17 [2780 kB] Fetched 2780 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0yi_v3fc/libstdc++-15-dev_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.32 [933 kB] Fetched 933 kB in 0s (66.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyn2hmez5/debhelper_13.32_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2.1 [30.9 kB] Fetched 30.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf5qq206u/libkrb5support0_1.22.1-2.1_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/tmpy8p64bjp/libxdmcp6_1.1.5-2+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1zpzy471/pkg-config_2.5.1-4_amd64.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/tmpx1uu248_/libxxhash0_0.8.3-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-16 [622 kB] Fetched 622 kB in 0s (50.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa1fbw81c/libc-bin_2.42-16_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 (94.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprudhdq_x/perl-base_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-1 [166 kB] Fetched 166 kB in 0s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0u1awbfa/libhwloc15_2.14.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-4 [700 kB] Fetched 700 kB in 0s (63.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6n7l1d66/findutils_4.10.0-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.26-1 [2311 kB] Fetched 2311 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa38nqn1w/gettext_0.26-1_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/tmpouwi2xo7/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-1 [383 kB] Fetched 383 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdbmparr1/ibverbs-providers_63.0-1_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 (57.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm05hnouj/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6z9785mw/dwz_0.16-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2.1 [78.8 kB] Fetched 78.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegnsrcfj/libk5crypto3_1.22.1-2.1_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/tmpzk91xmxh/libfido2-1_1.17.0-1_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 (29.7 MB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpcoyym0rb/libgmpxx4ldbl_6.3.0+dfsg-5+b2_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 (55.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1cwkakos/libdpkg-perl_1.23.7_all.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 (15.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zdjx2cf/libltdl-dev_2.5.4-11_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/tmpjm0n8inp/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 261~rc3-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsjhjt99r/libudev1_261~rc3-1_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 (74.6 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp_badip1q/zlib1g-dev_1.3.dfsg+really1.3.2-3_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 (1537 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbf_u71q6/libnuma1_2.0.19-1+b2_amd64.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 (52.0 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpc8tj8v5c/libgmp-dev_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b2 [63.8 kB] Fetched 63.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpim6bjl91/libproc2-0_4.0.4-9+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 (56.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcz1h7131/libhsa-runtime64-1_6.4.3+dfsg-5_amd64.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/tmpy_c3aks5/sysvinit-utils_3.18-1_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 (46.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuotivef6/googletest_1.17.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 binutils-common amd64 2.46-3 [2632 kB] Fetched 2632 kB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdzucxvqg/binutils-common_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-dev amd64 2.4.134-1 [305 kB] Fetched 305 kB in 0s (26.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphk1kbwml/libdrm-dev_2.4.134-1_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 (29.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnyn13o9p/m4_1.4.21-1_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/tmpc0u2lbuh/libxext6_1.3.4-1+b4_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/tmpaknkw8ud/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-1 [23.3 kB] Fetched 23.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz6_0_0ge/libdrm-amdgpu1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-3 [1559 kB] Fetched 1559 kB in 0s (89.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0xgaft_7/bash_5.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-1 [43.0 kB] Fetched 43.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp71bzz0ik/libibmad5_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.134-1 [19.3 kB] Fetched 19.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp62i4mhqh/libdrm-nouveau2_2.4.134-1_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 (71.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp94dykgg7/libopenmpi-dev_5.0.10-1_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/tmppjuje2r9/pkgconf_2.5.1-4_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/tmpnpqi4m91/libnl-route-3-200_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2.1 [335 kB] Fetched 335 kB in 0s (32.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppj_jo2v3/libkrb5-3_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-17 [542 kB] Fetched 542 kB in 0s (46.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6zz9gjld/gcc-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.1-3 [99.7 kB] Fetched 99.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppbupnff4/bsdextrautils_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.26-1 [802 kB] Fetched 802 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqobe6rb/autopoint_0.26-1_all.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 (171 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp293ew_xj/libboost1.90-dev_1.90.0-6_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 (98.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp0cf4nfm/libopenmpi40_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp0.8 amd64 0.8.0+dfsg-9+b1 [130 kB] Fetched 130 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvdalbj2/libyaml-cpp0.8_0.8.0+dfsg-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4gjgnjeb/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (6708 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppup849ic/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261~rc3-1 [3498 kB] Fetched 3498 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6l59d1ek/systemd_261~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-17 [2718 kB] Fetched 2718 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9o3nr3fh/libgcc-15-dev_15.2.0-17_amd64.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/tmptmn5lv9r/librhash1_1.4.6-1.1+b1_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 (0 B/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpdwk7j1ia/libmagic-mgc_5.47-4_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 (31.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeorovdhi/liblzma5_5.8.3-1_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/tmpmgk4z1c_/gcc-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3p3ikfsu/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-4 [25.2 kB] Fetched 25.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsz14oi3l/libffi8_3.5.2-4_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 (37.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoxkvup55/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42.1-3 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcrhvefqx/libsmartcols1_2.42.1-3_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/tmpo04tfvre/mpi-default-dev_1.20_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16.1.0-1 [1281 kB] Fetched 1281 kB in 0s (91.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi95kg8v3/liblsan0_16.1.0-1_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 (134 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcmv784j1/libperl5.40_5.40.1-8_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 (66.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplyr3nmcj/libeigen3-dev_3.4.0-5_all.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/tmpe22gqkkw/chrpath_0.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-1 [71.7 kB] Fetched 71.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjsq14afh/librdmacm1t64_63.0-1_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 (132 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4tyddymc/perl-modules-5.40_5.40.1-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.7-1 [361 kB] Fetched 361 kB in 0s (33.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsmmxzf2g/libarchive13t64_3.8.7-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.20.1-1 [954 kB] Fetched 954 kB in 0s (64.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpif7jrrej/libucx0_1.20.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b2 [880 kB] Fetched 880 kB in 0s (71.8 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp4i_yprm8/procps_4.0.4-9+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 (161 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxssyagxl/libamdhip64-6_6.4.3-5_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/tmp72_p3q3u/libbsd0_0.12.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b1 [670 kB] Fetched 670 kB in 0s (55.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9zyenmau/libpmix2t64_6.0.0+really5.0.9-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.32 [76.8 kB] Fetched 76.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnef2ump3/libdebhelper-perl_13.32_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-1 [695 kB] Fetched 695 kB in 0s (62.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmtaf0kjg/libibverbs-dev_63.0-1_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/tmp7zheqs08/zlib1g_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (39.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpas08a681/grep_3.12-1_amd64.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb_rd6wle/libcbor0.10_0.10.2-2.1+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 (62.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcv67l3jt/xz-utils_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-17 [28.0 kB] Fetched 28.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxkso8d2k/g++-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42.1-3 [1226 kB] Fetched 1226 kB in 0s (82.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkrn1v9t3/util-linux_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.6.2-1 [2482 kB] Fetched 2482 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqun0txut/libssl3t64_3.6.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 libgprofng0 amd64 2.46-3 [820 kB] Fetched 820 kB in 0s (63.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwpgnc95z/libgprofng0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53n7kzey/libevent-core-2.1-7t64_2.1.12-stable-10+b2_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/tmpd9u1ect9/libcrypt1_4.5.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 libctf0 amd64 2.46-3 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp96af14as/libctf0_2.46-3_amd64.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp72g161mr/pkgconf-bin_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp-dev amd64 0.8.0+dfsg-9+b1 [170 kB] Fetched 170 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjbc96dm0/libyaml-cpp-dev_0.8.0+dfsg-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0qc5gml7/gzip_1.13-1_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/tmpiqp7qkv5/libidn2-0_2.3.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb538vw_o/dpkg_1.23.7_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/tmpdghpbeun/libgdbm6t64_1.26-1+b2_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/tmpkqzh9urq/openmpi-common_5.0.10-1_all.deb' Downloading dependency 1 of 270: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 2 of 270: libjansson4:amd64=2.14-2+b4 Downloading dependency 3 of 270: cpp:amd64=4:15.2.0-5+b1 Downloading dependency 4 of 270: libselinux1:amd64=3.10-1 Downloading dependency 5 of 270: openssh-client:amd64=1:10.3p1-4 Downloading dependency 6 of 270: base-passwd:amd64=3.6.8 Downloading dependency 7 of 270: groff-base:amd64=1.24.1-1 Downloading dependency 8 of 270: libevent-openssl-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 9 of 270: libitm1:amd64=16.1.0-1 Downloading dependency 10 of 270: help2man:amd64=1.49.3 Downloading dependency 11 of 270: libxau6:amd64=1:1.0.11-1+b2 Downloading dependency 12 of 270: autotools-dev:amd64=20240727.1+nmu1 Downloading dependency 13 of 270: libdrm-radeon1:amd64=2.4.134-1 Downloading dependency 14 of 270: libpam-modules:amd64=1.7.0-5+b2 Downloading dependency 15 of 270: libzstd1:amd64=1.5.7+dfsg-3+b2 Downloading dependency 16 of 270: gcc-16-base:amd64=16.1.0-1 Downloading dependency 17 of 270: libuchardet0:amd64=0.0.8-2+b2 Downloading dependency 18 of 270: libssh2-1t64:amd64=1.11.1-3 Downloading dependency 19 of 270: libasan8:amd64=16.1.0-1 Downloading dependency 20 of 270: libmount1:amd64=2.42.1-3 Downloading dependency 21 of 270: libze1:amd64=1.28.2-2 Downloading dependency 22 of 270: libdrm-intel1:amd64=2.4.134-1 Downloading dependency 23 of 270: libncl2:amd64=2.1.21+git20210811.b1213a7-6+b2 Downloading dependency 24 of 270: libnghttp2-14:amd64=1.69.0-1 Downloading dependency 25 of 270: gcc:amd64=4:15.2.0-5+b1 Downloading dependency 26 of 270: gettext-base:amd64=0.26-1 Downloading dependency 27 of 270: libldap2:amd64=2.6.10+dfsg-1+b2 Downloading dependency 28 of 270: rpcsvc-proto:amd64=1.4.4-1 Downloading dependency 29 of 270: libstdc++6:amd64=16.1.0-1 Downloading dependency 30 of 270: libucc1:amd64=1.7.0~rc1-1 Downloading dependency 31 of 270: libz3-4:amd64=4.13.3-1.1 Downloading dependency 32 of 270: libsystemd-shared:amd64=261~rc3-1 Downloading dependency 33 of 270: man-db:amd64=2.13.1-1 Downloading dependency 34 of 270: libdrm2:amd64=2.4.134-1 Downloading dependency 35 of 270: libsasl2-2:amd64=2.1.28+dfsg1-11 Downloading dependency 36 of 270: libllvm21:amd64=1:21.1.8-7+b1 Downloading dependency 37 of 270: libsprng2-dev:amd64=2.0a-19 Downloading dependency 38 of 270: libcom-err2:amd64=1.47.4-1 Downloading dependency 39 of 270: libstdc++-15-dev:amd64=15.2.0-17 Downloading dependency 40 of 270: debhelper:amd64=13.32 Downloading dependency 41 of 270: libkrb5support0:amd64=1.22.1-2.1 Downloading dependency 42 of 270: libxdmcp6:amd64=1:1.1.5-2+b1 Downloading dependency 43 of 270: pkg-config:amd64=2.5.1-4 Downloading dependency 44 of 270: libxxhash0:amd64=0.8.3-2+b2 Downloading dependency 45 of 270: libc-bin:amd64=2.42-16 Downloading dependency 46 of 270: perl-base:amd64=5.40.1-8 Downloading dependency 47 of 270: libhwloc15:amd64=2.14.0-1 Downloading dependency 48 of 270: findutils:amd64=4.10.0-4 Downloading dependency 49 of 270: gettext:amd64=0.26-1 Downloading dependency 50 of 270: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 51 of 270: 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dependency 67 of 270: googletest:amd64=1.17.0-1 Downloading dependency 68 of 270: binutils-common:amd64=2.46-3 Downloading dependency 69 of 270: libdrm-dev:amd64=2.4.134-1 Downloading dependency 70 of 270: m4:amd64=1.4.21-1 Downloading dependency 71 of 270: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 72 of 270: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 73 of 270: libdrm-amdgpu1:amd64=2.4.134-1 Downloading dependency 74 of 270: bash:amd64=5.3-3 Downloading dependency 75 of 270: libibmad5:amd64=63.0-1 Downloading dependency 76 of 270: libdrm-nouveau2:amd64=2.4.134-1 Downloading dependency 77 of 270: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 78 of 270: pkgconf:amd64=2.5.1-4 Downloading dependency 79 of 270: libnl-route-3-200:amd64=3.12.0-2+b1 Downloading dependency 80 of 270: libkrb5-3:amd64=1.22.1-2.1 Downloading dependency 81 of 270: gcc-15:amd64=15.2.0-17 Downloading dependency 82 of 270: bsdextrautils:amd64=2.42.1-3 Downloading dependency 83 of 270: autopoint:amd64=0.26-1 Downloading dependency 84 of 270: libboost1.90-dev:amd64=1.90.0-6 Downloading dependency 85 of 270: libopenmpi40:amd64=5.0.10-1 Downloading dependency 86 of 270: libyaml-cpp0.8:amd64=0.8.0+dfsg-9+b1 Downloading dependency 87 of 270: coreutils:amd64=9.10-1 Downloading dependency 88 of 270: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 89 of 270: systemd:amd64=261~rc3-1 Downloading dependency 90 of 270: libgcc-15-dev:amd64=15.2.0-17 Downloading dependency 91 of 270: librhash1:amd64=1.4.6-1.1+b1 Downloading dependency 92 of 270: libmagic-mgc:amd64=1:5.47-4 Downloading dependency 93 of 270: liblzma5:amd64=5.8.3-1 Downloading dependency 94 of 270: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 95 of 270: hostname:amd64=3.25 Downloading dependency 96 of 270: libffi8:amd64=3.5.2-4 Downloading dependency 97 of 270: make:amd64=4.4.1-3 Downloading dependency 98 of 270: libsmartcols1:amd64=2.42.1-3 Downloading dependency 99 of 270: mpi-default-dev:amd64=1.20 Downloading dependency 100 of 270: liblsan0:amd64=16.1.0-1 Downloading dependency 101 of 270: libperl5.40:amd64=5.40.1-8 Downloading dependency 102 of 270: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 103 of 270: chrpath:amd64=0.18-1 Downloading dependency 104 of 270: librdmacm1t64:amd64=63.0-1 Downloading dependency 105 of 270: perl-modules-5.40:amd64=5.40.1-8 Downloading dependency 106 of 270: libarchive13t64:amd64=3.8.7-1 Downloading dependency 107 of 270: libucx0:amd64=1.20.1-1 Downloading dependency 108 of 270: procps:amd64=2:4.0.4-9+b2 Downloading dependency 109 of 270: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 110 of 270: libbsd0:amd64=0.12.2-3 Downloading dependency 111 of 270: libpmix2t64:amd64=6.0.0+really5.0.9-3+b1 Downloading dependency 112 of 270: libdebhelper-perl:amd64=13.32 Downloading dependency 113 of 270: libibverbs-dev:amd64=63.0-1 Downloading dependency 114 of 270: zlib1g:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 115 of 270: grep:amd64=3.12-1 Downloading dependency 116 of 270: libcbor0.10:amd64=0.10.2-2.1+b1 Downloading dependency 117 of 270: xz-utils:amd64=5.8.3-1 Downloading dependency 118 of 270: g++-15:amd64=15.2.0-17 Downloading dependency 119 of 270: util-linux:amd64=2.42.1-3 Downloading dependency 120 of 270: libssl3t64:amd64=3.6.2-1 Downloading dependency 121 of 270: libgprofng0:amd64=2.46-3 Downloading dependency 122 of 270: libevent-core-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 123 of 270: libcrypt1:amd64=1:4.5.1-1+b1 Downloading dependency 124 of 270: libctf0:amd64=2.46-3 Downloading dependency 125 of 270: pkgconf-bin:amd64=2.5.1-4 Downloading dependency 126 of 270: libyaml-cpp-dev:amd64=0.8.0+dfsg-9+b1 Downloading dependency 127 of 270: gzip:amd64=1.13-1 Downloading dependency 128 of 270: libidn2-0:amd64=2.3.8-5 Downloading dependency 129 of 270: dpkg:amd64=1.23.7 Downloading dependency 130 of 270: libgdbm6t64:amd64=1.26-1+b2 Downloading dependency 131 of 270: openmpi-common:amd64=5.0.10-1 Downloading dependency 132 of 270: libdebconfclient0:amd64=0.283Get: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/tmpyydfupp0/libdebconfclient0_0.283_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 linux-libc-dev all 7.0.10-1 [1994 kB] Fetched 1994 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf1ezzgtw/linux-libc-dev_7.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b2 [66.3 kB] Fetched 66.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf9vxve7d/libpam0g_1.7.0-5+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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzrf5hg_k/liblocale-gettext-perl_1.07-10_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 (9050 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6cu3yl9_/libedit2_3.1-20260512-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp90tz5nz2/ncurses-base_6.6+20251231-1_all.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/tmpg5di2vm5/libfile-stripnondeterminism-perl_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b2 [45.6 kB] Fetched 45.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppr2r7e2h/libpam-modules-bin_1.7.0-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42.1-3 [172 kB] Fetched 172 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7l1mufq/libblkid1_2.42.1-3_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/tmp5ga0iexx/libnuma-dev_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Fetched 59.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8vfbrwfy/libpsl5t64_0.21.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-17 [886 kB] Fetched 886 kB in 0s (72.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1uul0883/libgfortran-15-dev_15.2.0-17_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/tmpizw6mped/patch_2.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 binutils-x86-64-linux-gnu amd64 2.46-3 [1058 kB] Fetched 1058 kB in 0s (72.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcdksli7n/binutils-x86-64-linux-gnu_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-17 [13.2 MB] Fetched 13.2 MB in 0s (167 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu6qudsov/g++-15-x86-64-linux-gnu_15.2.0-17_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 (31.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb0sipu_y/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Fetched 184 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe9crfl5d/libevent-2.1-7t64_2.1.12-stable-10+b2_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/tmpyr38i3g8/base-files_14.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6+b2 [598 kB] Fetched 598 kB in 0s (2076 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53nqsbk4/libncl-dev_2.1.21+git20210811.b1213a7-6+b2_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/tmpifqkzg18/libnl-3-200_3.12.0-2+b1_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/tmpskwd61hc/libpkgconf7_2.5.1-4_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 (40.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5zl88_sw/libprrte3_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 16.1.0-1 [148 kB] Fetched 148 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe8eptwlc/libquadmath0_16.1.0-1_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 (42.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7c6az5dz/libunistring5_1.4.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-3 [331 kB] Fetched 331 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplfqf0xda/sed_4.9-3_amd64.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/tmpbpaghk_b/time_1.10-0.1_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 (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp8filafwi/libmagic1t64_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.3-1 [16.2 MB] Fetched 16.2 MB in 0s (171 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgch9wiq6/cmake_4.3.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2.1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy7fms815/libgssapi-krb5-2_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp79t4we1k/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Fetched 54.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3p74ezzh/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6cbbes61/libmpc3_1.3.1-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvf55qjt/libnl-3-dev_3.12.0-2+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpquadayha/libpcre2-8-0_10.46-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 261~rc3-1 [467 kB] Fetched 467 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyvbat8lu/libsystemd0_261~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-1 [24.7 kB] Fetched 24.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ueht4_o/libhwloc-plugins_2.14.0-1_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 (34.2 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmp_nu39q94/libx11-data_1.8.13-1_all.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 (62.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr8xx22c3/libfabric1_2.1.0-1.1+b2_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 (52.3 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp4j_fdwz7/libgmp10_6.3.0+dfsg-5+b2_amd64.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/tmpbcwmr2zt/debianutils_5.23.2_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/tmppsy6s5ax/g++_15.2.0-5+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjidarzrs/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.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 (128 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsrkwilfq/libprrte-dev_3.0.13-3_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/tmpo1tb6_ys/libkeyutils1_1.6.3-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian 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/tmpx9ds0gx8/libngtcp2-crypto-ossl0_1.22.1-1_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/tmpdrcmzool/libxcb1_1.17.0-2+b2_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/tmp1xah8fmz/bzip2_1.0.8-6+b2_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 (46.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp97s9effe/libsimde-dev_0.8.4~rc3-5_all.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/tmp8inccd3r/liblz4-1_1.10.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16.1.0-1 [2572 kB] Fetched 2572 kB in 0s (125 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp646ediy5/libtsan2_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp4vajcw5x/libattr1_2.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-1 [878 kB] Fetched 878 kB in 0s (70.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnzhctc1e/libgfortran5_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16.1.0-1 [1136 kB] Fetched 1136 kB in 0s (83.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps9p7vd46/libubsan1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 16.1.0-1 [10.4 kB] Fetched 10.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6fvg9fkv/libatomic1_16.1.0-1_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/tmps59kryhs/libxnvctrl0_535.171.04-1+b3_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 (60.4 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmpaqv3i8wm/automake_1.18.1-4_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fet_wn6/dh-strip-nondeterminism_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-17 [12.8 MB] Fetched 12.8 MB in 0s (160 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqy02o5_6/gfortran-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-1 [62.6 kB] Fetched 62.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqa7o90pn/libibverbs1_63.0-1_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/tmp84xwor37/libmd0_1.2.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-16 [1098 kB] Fetched 1098 kB in 0s (76.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0v__99n7/libc-gconv-modules-extra_2.42-16_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/tmp30_2vmzg/init-system-helpers_1.69_all.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx664fs_f/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 libctf-nobfd0 amd64 2.46-3 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpct_4zu9u/libctf-nobfd0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 16.1.0-1 [74.0 kB] Fetched 74.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ch11caf/libgcc-s1_16.1.0-1_amd64.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/tmpiqa0c1mw/perl_5.40.1-8_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 (40.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp75jr659p/libltdl7_2.5.4-11_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/tmpzja9ymt3/file_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-17 [36.8 kB] Fetched 36.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvd7ix3cj/gcc-15-base_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Fetched 308 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyruejnb8/libevent-dev_2.1.12-stable-10+b2_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 (186 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp95o_vqj2/libamd-comgr3_7.0.2+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1+b1 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpebg6uswd/libncursesw6_6.6+20251231-1+b1_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/tmpo1wsgxy7/libsasl2-modules-db_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42.1-3 [33.3 kB] Fetched 33.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqhpzavxo/libuuid1_2.42.1-3_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/tmpcvzhh6h7/libfuse3-4_3.18.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5g6qwy0f/libpam-runtime_1.7.0-5_all.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 (58.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpihfm878e/libdb5.3t64_5.3.28+dfsg2-11+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaahp5ay6/libmunge2_0.5.18-1_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/tmpm67caktq/libprrte-bin_3.0.13-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy_cuyj7m/libnettle8t64_3.10.2-1+b1_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/tmpa_fynszn/libpipeline1_1.5.8-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-16 [1789 kB] Fetched 1789 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1amfza51/libc6_2.42-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-17 [20.8 kB] Fetched 20.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ox3v0ta/gfortran-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-17 [12.1 MB] Fetched 12.1 MB in 0s (171 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoy6nt70b/cpp-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 binutils amd64 2.46-3 [282 kB] Fetched 282 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps4yz6ety/binutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-17 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfxzrf8rq/cpp-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.42.1-3 [164 kB] Fetched 164 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpezhtrlab/mount_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.7-2 [86.5 kB] Fetched 86.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjk6rwgp9/libjsoncpp26_1.9.7-2_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/tmp5krfpn94/libelf1t64_0.195-1_amd64.deb' Get:1 http://deb.debian.org/debian 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/tmpsq6360zn/libngtcp2-16_1.22.1-1_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/tmp9li153ei/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (98.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa_i8sdgy/dpkg-dev_1.23.7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 libbinutils amd64 2.46-3 [548 kB] Fetched 548 kB in 0s (52.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3iidq7kv/libbinutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-1 [260 kB] Fetched 260 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiembg7we/libhwloc-dev_2.14.0-1_amd64.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 (70.7 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpqdziuyrz/libx11-6_1.8.13-1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzj8d10zf/libsprng2_2.0a-19_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 (66.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn6t6_p81/libmpfr6_4.2.2-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_wzx4bi3/ocl-icd-libopencl1_2.3.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Fetched 52.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzc8hurua/libpciaccess0_0.17-3+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxexcgiom/libacl1_2.3.2-3_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/tmpb_nx05ya/mawk_1.3.4.20260302-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-16 [1996 kB] Fetched 1996 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe2zk8ted/libc6-dev_2.42-16_amd64.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/tmpgzcg99z9/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (63.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7cglqv2p/libisl23_0.27-2_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/tmppkdsbh6s/libpsm2-2_11.2.185-2.1_amd64.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3bllud_h/libgdbm-compat4t64_1.26-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1+b1 [350 kB] Fetched 350 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3q9ua7l3/libtinfo6_6.6+20251231-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-1 [28.3 kB] Fetched 28.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7izxks6o/libibumad3_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1+b1 [442 kB] Fetched 442 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxk5w59ow/ncurses-bin_6.6+20251231-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.20.0-5 [409 kB] Fetched 409 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo6k7w3uj/libcurl4t64_8.20.0-5_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/tmp86x28qnh/dash_0.5.12-12_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/tmpj3uthv90/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16.1.0-1 [1580 kB] Fetched 1580 kB in 0s (86.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffrznuru/libhwasan0_16.1.0-1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe777uovm/sensible-utils_0.0.26_all.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 (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzmh4zxcc/cpp-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-16 [37.9 kB] Fetched 37.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnbacsn4d/libc-dev-bin_2.42-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Fetched 516 kB in 0s (50.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsajv1s_t/autoconf_2.73-2_all.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/tmp0_bhrwom/debconf_1.5.92_all.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/tmp8r4xstwo/libboost-dev_1.90.0.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 16.1.0-1 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2zopxzoc/libgomp1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp29xhl56f/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_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 (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpkifj16yc/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 16.1.0-1 [46.1 kB] Fetched 46.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpicbmvww9/libcc1-0_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-1 [7808 B] Fetched 7808 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2h7cj9lb/libdrm-common_2.4.134-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (52.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6h5z3p2b/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.3-1 [17.9 kB] Fetched 17.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy7wur3ki/libcap-ng0_0.9.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260611T143613Z forky/main amd64 libsframe3 amd64 2.46-3 [84.7 kB] Fetched 84.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0nf0zstt/libsframe3_2.46-3_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) Downloading dependency 133 of 270: linux-libc-dev:amd64=7.0.10-1 Downloading dependency 134 of 270: libpam0g:amd64=1.7.0-5+b2 Downloading dependency 135 of 270: liblocale-gettext-perl:amd64=1.07-10 Downloading dependency 136 of 270: libedit2:amd64=3.1-20260512-1 Downloading dependency 137 of 270: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 138 of 270: libfile-stripnondeterminism-perl:amd64=1.15.1-1 Downloading dependency 139 of 270: libpam-modules-bin:amd64=1.7.0-5+b2 Downloading dependency 140 of 270: libblkid1:amd64=2.42.1-3 Downloading dependency 141 of 270: libnuma-dev:amd64=2.0.19-1+b2 Downloading dependency 142 of 270: libpsl5t64:amd64=0.21.5-1 Downloading dependency 143 of 270: libgfortran-15-dev:amd64=15.2.0-17 Downloading dependency 144 of 270: patch:amd64=2.8-2 Downloading dependency 145 of 270: binutils-x86-64-linux-gnu:amd64=2.46-3 Downloading dependency 146 of 270: g++-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 147 of 270: libbrotli1:amd64=1.2.0-3 Downloading dependency 148 of 270: libevent-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 149 of 270: base-files:amd64=14.2 Downloading dependency 150 of 270: libncl-dev:amd64=2.1.21+git20210811.b1213a7-6+b2 Downloading dependency 151 of 270: libnl-3-200:amd64=3.12.0-2+b1 Downloading dependency 152 of 270: libpkgconf7:amd64=2.5.1-4 Downloading dependency 153 of 270: libprrte3:amd64=3.0.13-3 Downloading dependency 154 of 270: libquadmath0:amd64=16.1.0-1 Downloading dependency 155 of 270: libunistring5:amd64=1.4.2-1 Downloading dependency 156 of 270: sed:amd64=4.9-3 Downloading dependency 157 of 270: time:amd64=1.10-0.1 Downloading dependency 158 of 270: libmagic1t64:amd64=1:5.47-4 Downloading dependency 159 of 270: cmake:amd64=4.3.3-1 Downloading dependency 160 of 270: libgssapi-krb5-2:amd64=1.22.1-2.1 Downloading dependency 161 of 270: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 162 of 270: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 163 of 270: libmpc3:amd64=1.3.1-3 Downloading dependency 164 of 270: libnl-3-dev:amd64=3.12.0-2+b1 Downloading dependency 165 of 270: libpcre2-8-0:amd64=10.46-1+b2 Downloading dependency 166 of 270: libsystemd0:amd64=261~rc3-1 Downloading dependency 167 of 270: libhwloc-plugins:amd64=2.14.0-1 Downloading dependency 168 of 270: libx11-data:amd64=2:1.8.13-1 Downloading dependency 169 of 270: libfabric1:amd64=2.1.0-1.1+b2 Downloading dependency 170 of 270: libgmp10:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 171 of 270: debianutils:amd64=5.23.2 Downloading dependency 172 of 270: g++:amd64=4:15.2.0-5+b1 Downloading dependency 173 of 270: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 174 of 270: libprrte-dev:amd64=3.0.13-3 Downloading dependency 175 of 270: libkeyutils1:amd64=1.6.3-6+b2 Downloading dependency 176 of 270: libngtcp2-crypto-ossl0:amd64=1.22.1-1 Downloading dependency 177 of 270: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 178 of 270: 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libmunge2:amd64=0.5.18-1 Downloading dependency 210 of 270: libprrte-bin:amd64=3.0.13-3 Downloading dependency 211 of 270: libnettle8t64:amd64=3.10.2-1+b1 Downloading dependency 212 of 270: libpipeline1:amd64=1.5.8-3 Downloading dependency 213 of 270: libc6:amd64=2.42-16 Downloading dependency 214 of 270: gfortran-15:amd64=15.2.0-17 Downloading dependency 215 of 270: cpp-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 216 of 270: binutils:amd64=2.46-3 Downloading dependency 217 of 270: cpp-15:amd64=15.2.0-17 Downloading dependency 218 of 270: mount:amd64=2.42.1-3 Downloading dependency 219 of 270: libjsoncpp26:amd64=1.9.7-2 Downloading dependency 220 of 270: libelf1t64:amd64=0.195-1 Downloading dependency 221 of 270: libngtcp2-16:amd64=1.22.1-1 Downloading dependency 222 of 270: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 223 of 270: dpkg-dev:amd64=1.23.7 Downloading dependency 224 of 270: libbinutils:amd64=2.46-3 Downloading dependency 225 of 270: libhwloc-dev:amd64=2.14.0-1 Downloading dependency 226 of 270: libx11-6:amd64=2:1.8.13-1 Downloading dependency 227 of 270: libsprng2:amd64=2.0a-19 Downloading dependency 228 of 270: libmpfr6:amd64=4.2.2-3 Downloading dependency 229 of 270: ocl-icd-libopencl1:amd64=2.3.4-1+b1 Downloading dependency 230 of 270: libpciaccess0:amd64=0.17-3+b4 Downloading dependency 231 of 270: libacl1:amd64=2.3.2-3 Downloading dependency 232 of 270: mawk:amd64=1.3.4.20260302-1 Downloading dependency 233 of 270: libc6-dev:amd64=2.42-16 Downloading dependency 234 of 270: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 235 of 270: libisl23:amd64=0.27-2 Downloading dependency 236 of 270: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 237 of 270: libgdbm-compat4t64:amd64=1.26-1+b2 Downloading dependency 238 of 270: libtinfo6:amd64=6.6+20251231-1+b1 Downloading dependency 239 of 270: libibumad3:amd64=63.0-1 Downloading dependency 240 of 270: ncurses-bin:amd64=6.6+20251231-1+b1 Downloading dependency 241 of 270: libcurl4t64:amd64=8.20.0-5 Downloading dependency 242 of 270: dash:amd64=0.5.12-12 Downloading dependency 243 of 270: dh-autoreconf:amd64=22 Downloading dependency 244 of 270: libhwasan0:amd64=16.1.0-1 Downloading dependency 245 of 270: sensible-utils:amd64=0.0.26 Downloading dependency 246 of 270: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 247 of 270: libc-dev-bin:amd64=2.42-16 Downloading dependency 248 of 270: autoconf:amd64=2.73-2 Downloading dependency 249 of 270: debconf:amd64=1.5.92 Downloading dependency 250 of 270: libboost-dev:amd64=1.90.0.2 Downloading dependency 251 of 270: libgomp1:amd64=16.1.0-1 Downloading dependency 252 of 270: libevent-extra-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 253 of 270: diffutils:amd64=1:3.12-1 Downloading dependency 254 of 270: libcc1-0:amd64=16.1.0-1 Downloading dependency 255 of 270: libdrm-common:amd64=2.4.134-1 Downloading dependency 256 of 270: libtool:amd64=2.5.4-11 Downloading dependency 257 of 270: libcap-ng0:amd64=0.9.3-1 Downloading dependency 258 of 270: libsframe3:amd64=2.46-3 Downloading dependency 259 of 270: libuv1t64:amd64=1.52.1-4 Downloading dependency 260 of 270: libamd-smi26:amd64=7.2.0-3dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8hb1zno8/libuv1t64_1.52.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-smi26 amd64 7.2.0-3 [830 kB] Fetched 830 kB in 0s (60.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkbx8bit2/libamd-smi26_7.2.0-3_amd64.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/tmp19u0c393/g++-x86-64-linux-gnu_15.2.0-5+b1_amd64.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 (54.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpefxvhi7y/libxml2-16_2.15.3+dfsg-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/tmp76gtygy8/po-debconf_1.0.22_all.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp38497wmh/libnl-route-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess-dev amd64 0.17-3+b4 [55.5 kB] Fetched 55.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_e4bmeqr/libpciaccess-dev_0.17-3+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b1 [767 kB] Fetched 767 kB in 0s (65.2 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpcad_elhq/libclang-common-21-dev_21.1.8-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.1-1 [117 kB] Fetched 117 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdp7dpxng/libexpat1_2.8.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-17 [23.4 MB] Fetched 23.4 MB in 0s (165 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp7oo3p91/gcc-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.6.2-1 [316 kB] Fetched 316 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgmoroosw/openssl-provider-legacy_3.6.2-1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0f_2z2vh/libbz2-1.0_1.0.8-6+b2_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/tmpcy76jc25/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.cDmjMIWfBE as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE 127.0.0.1 - - [12/Jun/2026 09:52:13] code 404, message File not found 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:42871 ./ InRelease 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:42871 ./ Release [462 B] 127.0.0.1 - - [12/Jun/2026 09:52:13] code 404, message File not found 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:42871 ./ Release.gpg 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:42871 ./ Packages [332 kB] Fetched 332 kB in 0s (19.8 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 - - [12/Jun/2026 09:52:13] "GET /./gcc-16-base_16.1.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libc-gconv-modules-extra_2.42-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libc6_2.42-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libgcc-s1_16.1.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./mawk_1.3.4.20260302-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./base-files_14.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libtinfo6_6.6%2b20251231-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./bash_5.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libpcre2-8-0_10.46-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libselinux1_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./zlib1g_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libssl3t64_3.6.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./openssl-provider-legacy_3.6.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libsystemd0_261%7erc3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./coreutils_9.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./diffutils_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libbz2-1.0_1.0.8-6%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./liblzma5_5.8.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libmd0_1.2.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./tar_1.35%2bdfsg-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./dpkg_1.23.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./findutils_4.10.0-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./grep_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./ncurses-bin_6.6%2b20251231-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libcrypt1_4.5.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./perl-base_5.40.1-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./sed_4.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libcap-ng0_0.9.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libpam0g_1.7.0-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libpam-modules-bin_1.7.0-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libpam-modules_1.7.0-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libblkid1_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libmount1_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libsmartcols1_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libudev1_261%7erc3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libuuid1_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./util-linux_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libdebconfclient0_0.283_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./libc-bin_2.42-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:13] "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.cDmjMIWfBE 127.0.0.1 - - [12/Jun/2026 09:52:14] code 404, message File not found 127.0.0.1 - - [12/Jun/2026 09:52:14] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:42871 ./ InRelease 127.0.0.1 - - [12/Jun/2026 09:52:14] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:42871 ./ Release 127.0.0.1 - - [12/Jun/2026 09:52:14] code 404, message File not found 127.0.0.1 - - [12/Jun/2026 09:52:14] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:42871 ./ 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.cDmjMIWfBE 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 - - [12/Jun/2026 09:52:34] "GET /./mount_2.42.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libsystemd-shared_261%7erc3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libnghttp3-9_1.15.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libngtcp2-16_1.22.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libbrotli1_1.2.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libkrb5support0_1.22.1-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libcom-err2_1.47.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libk5crypto3_1.22.1-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libkeyutils1_1.6.3-6%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libkrb5-3_1.22.1-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libgssapi-krb5-2_1.22.1-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libunistring5_1.4.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libidn2-0_2.3.8-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libsasl2-modules-db_2.1.28%2bdfsg1-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libsasl2-2_2.1.28%2bdfsg1-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libldap2_2.6.10%2bdfsg-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libnghttp2-14_1.69.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libngtcp2-crypto-ossl0_1.22.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:34] "GET /./libpsl5t64_0.21.5-1_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./ocl-icd-libopencl1_2.3.4-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libhwloc-plugins_2.14.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libpmix2t64_6.0.0%2breally5.0.9-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./openmpi-common_5.0.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libnl-3-dev_3.12.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libnl-route-3-dev_3.12.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libibverbs-dev_63.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libprrte3_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libjs-jquery_3.7.1%2bdfsg%2b%7e3.5.33-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libprrte-dev_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libnuma-dev_2.0.19-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libhwloc-dev_2.14.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libevent-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libevent-extra-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libevent-dev_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libprrte-bin_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libboost1.90-dev_1.90.0-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libyaml-cpp0.8_0.8.0%2bdfsg-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libeigen3-dev_3.4.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libyaml-cpp-dev_0.8.0%2bdfsg-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libncl-dev_2.1.21%2bgit20210811.b1213a7-6%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./time_1.10-0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./libboost-dev_1.90.0.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [12/Jun/2026 09:52:36] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpcy76jc25/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE Reading package lists... Building dependency tree... Reading state information... libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. libselinux1 is already the newest version (3.10-1). openssh-client is already the newest version (1:10.3p1-4). openssh-client set to manually installed. base-passwd is already the newest version (3.6.8). groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-openssl-2.1-7t64 set to manually installed. libitm1 is already the newest version (16.1.0-1). libitm1 set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. libdrm-radeon1 is already the newest version (2.4.134-1). libdrm-radeon1 set to manually installed. libpam-modules is already the newest version (1.7.0-5+b2). libzstd1 is already the newest version (1.5.7+dfsg-3+b2). gcc-16-base is already the newest version (16.1.0-1). libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-3). libssh2-1t64 set to manually installed. libasan8 is already the newest version (16.1.0-1). libasan8 set to manually installed. libmount1 is already the newest version (2.42.1-3). libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. libdrm-intel1 is already the newest version (2.4.134-1). libdrm-intel1 set to manually installed. libncl2 is already the newest version (2.1.21+git20210811.b1213a7-6+b2). libncl2 set to manually installed. libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. gcc is already the newest version (4:15.2.0-5+b1). gcc set to manually installed. gettext-base is already the newest version (0.26-1). gettext-base set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b2). libldap2 set to manually installed. rpcsvc-proto is already the newest version (1.4.4-1). rpcsvc-proto set to manually installed. libstdc++6 is already the newest version (16.1.0-1). libstdc++6 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. libz3-4 is already the newest version (4.13.3-1.1). libz3-4 set to manually installed. libsystemd-shared is already the newest version (261~rc3-1). libsystemd-shared set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. libdrm2 is already the newest version (2.4.134-1). libdrm2 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. libllvm21 is already the newest version (1:21.1.8-7+b1). libllvm21 set to manually installed. libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-17). libstdc++-15-dev set to manually installed. debhelper is already the newest version (13.32). debhelper set to manually installed. libkrb5support0 is already the newest version (1.22.1-2.1). libkrb5support0 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. libc-bin is already the newest version (2.42-16). perl-base is already the newest version (5.40.1-8). libhwloc15 is already the newest version (2.14.0-1). libhwloc15 set to manually installed. findutils is already the newest version (4.10.0-4). gettext is already the newest version (0.26-1). gettext set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. ibverbs-providers is already the newest version (63.0-1). ibverbs-providers set to manually installed. tar is already the newest version (1.35+dfsg-4). dwz is already the newest version (0.16-4). dwz set to manually installed. libk5crypto3 is already the newest version (1.22.1-2.1). libk5crypto3 set to manually installed. libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b2). libgmpxx4ldbl set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libudev1 is already the newest version (261~rc3-1). zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.2-3). zlib1g-dev set to manually installed. libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b2). libgmp-dev set to manually installed. libproc2-0 is already the newest version (2:4.0.4-9+b2). libproc2-0 set to manually installed. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. sysvinit-utils is already the newest version (3.18-1). googletest is already the newest version (1.17.0-1). googletest set to manually installed. binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. libdrm-dev is already the newest version (2.4.134-1). libdrm-dev set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libdrm-amdgpu1 is already the newest version (2.4.134-1). libdrm-amdgpu1 set to manually installed. bash is already the newest version (5.3-3). libibmad5 is already the newest version (63.0-1). libibmad5 set to manually installed. libdrm-nouveau2 is already the newest version (2.4.134-1). libdrm-nouveau2 set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. libnl-route-3-200 is already the newest version (3.12.0-2+b1). libnl-route-3-200 set to manually installed. libkrb5-3 is already the newest version (1.22.1-2.1). libkrb5-3 set to manually installed. gcc-15 is already the newest version (15.2.0-17). gcc-15 set to manually installed. bsdextrautils is already the newest version (2.42.1-3). bsdextrautils set to manually installed. autopoint is already the newest version (0.26-1). autopoint set to manually installed. libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libyaml-cpp0.8 is already the newest version (0.8.0+dfsg-9+b1). libyaml-cpp0.8 set to manually installed. coreutils is already the newest version (9.10-1). libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. systemd is already the newest version (261~rc3-1). systemd set to manually installed. libgcc-15-dev is already the newest version (15.2.0-17). libgcc-15-dev set to manually installed. librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. libmagic-mgc is already the newest version (1:5.47-4). libmagic-mgc set to manually installed. liblzma5 is already the newest version (5.8.3-1). 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. hostname is already the newest version (3.25). libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libsmartcols1 is already the newest version (2.42.1-3). mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. liblsan0 is already the newest version (16.1.0-1). liblsan0 set to manually installed. libperl5.40 is already the newest version (5.40.1-8). libperl5.40 set to manually installed. libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. chrpath is already the newest version (0.18-1). chrpath set to manually installed. librdmacm1t64 is already the newest version (63.0-1). librdmacm1t64 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. libarchive13t64 is already the newest version (3.8.7-1). libarchive13t64 set to manually installed. libucx0 is already the newest version (1.20.1-1). libucx0 set to manually installed. procps is already the newest version (2:4.0.4-9+b2). procps set to manually installed. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libbsd0 is already the newest version (0.12.2-3). libbsd0 set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b1). libpmix2t64 set to manually installed. libdebhelper-perl is already the newest version (13.32). libdebhelper-perl set to manually installed. libibverbs-dev is already the newest version (63.0-1). libibverbs-dev set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). grep is already the newest version (3.12-1). libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. g++-15 is already the newest version (15.2.0-17). g++-15 set to manually installed. util-linux is already the newest version (2.42.1-3). libssl3t64 is already the newest version (3.6.2-1). libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-core-2.1-7t64 set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. libyaml-cpp-dev is already the newest version (0.8.0+dfsg-9+b1). libyaml-cpp-dev set to manually installed. gzip is already the newest version (1.13-1). libidn2-0 is already the newest version (2.3.8-5). libidn2-0 set to manually installed. dpkg is already the newest version (1.23.7). libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. libdebconfclient0 is already the newest version (0.283). linux-libc-dev is already the newest version (7.0.10-1). linux-libc-dev set to manually installed. libpam0g is already the newest version (1.7.0-5+b2). liblocale-gettext-perl is already the newest version (1.07-10). liblocale-gettext-perl set to manually installed. libedit2 is already the newest version (3.1-20260512-1). libedit2 set to manually installed. ncurses-base is already the newest version (6.6+20251231-1). libfile-stripnondeterminism-perl is already the newest version (1.15.1-1). libfile-stripnondeterminism-perl set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b2). libblkid1 is already the newest version (2.42.1-3). libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. libpsl5t64 is already the newest version (0.21.5-1). libpsl5t64 set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-17). libgfortran-15-dev set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46-3). binutils-x86-64-linux-gnu set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.2.0-17). g++-15-x86-64-linux-gnu set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. base-files is already the newest version (14.2). libncl-dev is already the newest version (2.1.21+git20210811.b1213a7-6+b2). libncl-dev set to manually installed. libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. libquadmath0 is already the newest version (16.1.0-1). libquadmath0 set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. sed is already the newest version (4.9-3). time is already the newest version (1.10-0.1). time set to manually installed. libmagic1t64 is already the newest version (1:5.47-4). libmagic1t64 set to manually installed. cmake is already the newest version (4.3.3-1). cmake set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-2.1). libgssapi-krb5-2 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b2). libsystemd0 is already the newest version (261~rc3-1). libhwloc-plugins is already the newest version (2.14.0-1). libhwloc-plugins set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b2). debianutils is already the newest version (5.23.2). g++ is already the newest version (4:15.2.0-5+b1). g++ 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. libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.22.1-1). libngtcp2-crypto-ossl0 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. libtsan2 is already the newest version (16.1.0-1). libtsan2 set to manually installed. libattr1 is already the newest version (1:2.5.2-4). libgfortran5 is already the newest version (16.1.0-1). libgfortran5 set to manually installed. libubsan1 is already the newest version (16.1.0-1). libubsan1 set to manually installed. libatomic1 is already the newest version (16.1.0-1). libatomic1 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. automake is already the newest version (1:1.18.1-4). automake set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.1-1). dh-strip-nondeterminism set to manually installed. gfortran-15-x86-64-linux-gnu is already the newest version (15.2.0-17). gfortran-15-x86-64-linux-gnu set to manually installed. libibverbs1 is already the newest version (63.0-1). libibverbs1 set to manually installed. libmd0 is already the newest version (1.2.0-2). libc-gconv-modules-extra is already the newest version (2.42-16). init-system-helpers is already the newest version (1.69). openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. libgcc-s1 is already the newest version (16.1.0-1). perl is already the newest version (5.40.1-8). perl set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. file is already the newest version (1:5.47-4). file set to manually installed. gcc-15-base is already the newest version (15.2.0-17). gcc-15-base set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1+b1). libncursesw6 set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libuuid1 is already the newest version (2.42.1-3). libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. libc6 is already the newest version (2.42-16). gfortran-15 is already the newest version (15.2.0-17). gfortran-15 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-17). cpp-15-x86-64-linux-gnu set to manually installed. binutils is already the newest version (2.46-3). binutils set to manually installed. cpp-15 is already the newest version (15.2.0-17). cpp-15 set to manually installed. mount is already the newest version (2.42.1-3). mount set to manually installed. libjsoncpp26 is already the newest version (1.9.7-2). libjsoncpp26 set to manually installed. libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. libhwloc-dev is already the newest version (2.14.0-1). libhwloc-dev set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. libacl1 is already the newest version (2.3.2-3). mawk is already the newest version (1.3.4.20260302-1). libc6-dev is already the newest version (2.42-16). libc6-dev set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1+b1). libibumad3 is already the newest version (63.0-1). libibumad3 set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1+b1). libcurl4t64 is already the newest version (8.20.0-5). libcurl4t64 set to manually installed. dash is already the newest version (0.5.12-12). dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libhwasan0 is already the newest version (16.1.0-1). libhwasan0 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. 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. libc-dev-bin is already the newest version (2.42-16). libc-dev-bin set to manually installed. autoconf is already the newest version (2.73-2). autoconf set to manually installed. debconf is already the newest version (1.5.92). libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. libgomp1 is already the newest version (16.1.0-1). libgomp1 set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-extra-2.1-7t64 set to manually installed. diffutils is already the newest version (1:3.12-1). libcc1-0 is already the newest version (16.1.0-1). libcc1-0 set to manually installed. libdrm-common is already the newest version (2.4.134-1). libdrm-common set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. libcap-ng0 is already the newest version (0.9.3-1). libsframe3 is already the newest version (2.46-3). libsframe3 set to manually installed. libuv1t64 is already the newest version (1.52.1-4). libuv1t64 set to manually installed. libamd-smi26 is already the newest version (7.2.0-3). libamd-smi26 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. libxml2-16 is already the newest version (2.15.3+dfsg-1). libxml2-16 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf 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. libpciaccess-dev is already the newest version (0.17-3+b4). libpciaccess-dev set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7+b1). libclang-common-21-dev set to manually installed. libexpat1 is already the newest version (2.8.1-1). libexpat1 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-17). gcc-15-x86-64-linux-gnu set to manually installed. openssl-provider-legacy is already the newest version (3.6.2-1). libbz2-1.0 is already the newest version (1.0.8-6+b2). The following NEW packages will be installed: pkg-config 127.0.0.1 - - [12/Jun/2026 09:54:56] "GET /./pkg-config_2.5.1-4_amd64.deb HTTP/1.1" 200 - 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 18.1 kB of archives. After this operation, 34.8 kB of additional disk space will be used. Get:1 http://localhost:42871 ./ pkg-config 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (1715 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE/ Selecting previously unselected package pkg-config:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41632 files and directories currently installed.) Preparing to unpack .../pkg-config_2.5.1-4_amd64.deb ... Unpacking pkg-config:amd64 (2.5.1-4) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE/ Setting up pkg-config:amd64 (2.5.1-4) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE (Reading database ... 41637 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.cDmjMIWfBE I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.cDmjMIWfBE 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.cDmjMIWfBE... I: success in 170.8651 seconds Downloading dependency 261 of 270: g++-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 262 of 270: libxml2-16:amd64=2.15.3+dfsg-1 Downloading dependency 263 of 270: po-debconf:amd64=1.0.22 Downloading dependency 264 of 270: libnl-route-3-dev:amd64=3.12.0-2+b1 Downloading dependency 265 of 270: libpciaccess-dev:amd64=0.17-3+b4 Downloading dependency 266 of 270: libclang-common-21-dev:amd64=1:21.1.8-7+b1 Downloading dependency 267 of 270: libexpat1:amd64=2.8.1-1 Downloading dependency 268 of 270: gcc-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 269 of 270: openssl-provider-legacy:amd64=3.6.2-1 Downloading dependency 270 of 270: libbz2-1.0:amd64=1.0.8-6+b2 env --chdir=/srv/rebuilderd/tmp/rebuilderdzhXbrN/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1781036498 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildRtP01O/debrebuild.sbuildrc.JAs35MXBwtjv sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildRtP01O/debrebuild.tar.HEWEnKS6Nypm --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=iqtree3-3.1.1+dfsg /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+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 (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl41-amd64.novalocal +==============================================================================+ | iqtree3 3.1.1+dfsg-2 (amd64) Fri, 12 Jun 2026 09:55:05 +0000 | +==============================================================================+ Package: iqtree3 Version: 3.1.1+dfsg-2 Source Version: 3.1.1+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/debrebuildRtP01O/debrebuild.tar.HEWEnKS6Nypm to /srv/rebuilderd/tmp/tmp.sbuild.cOOHQ2qKL9... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Fri, 12 Jun 2026 09:55:10 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+dfsg-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Fri, 12 Jun 2026 09:55:11 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-LfyKVD/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Fri, 12 Jun 2026 09:55:14 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64) +------------------------------------------------------------------------------+ | Build environment Fri, 12 Jun 2026 09:55:14 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.90+deb13.1-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.90-2 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-17 gcc-15_15.2.0-17 libc6-dev_2.42-16 libstdc++-15-dev_15.2.0-17 libstdc++6_16.1.0-1 linux-libc-dev_7.0.10-1 Package versions: autoconf_2.73-2 automake_1:1.18.1-4 autopoint_0.26-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42.1-3 build-essential_12.12 bzip2_1.0.8-6+b2 chrpath_0.18-1 cmake_4.3.3-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_13.32 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_0.16-4 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-x86-64-linux-gnu_15.2.0-17 gcc-16-base_16.1.0-1 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_0.26-1 gettext-base_0.26-1 gfortran-15_15.2.0-17 gfortran-15-x86-64-linux-gnu_15.2.0-17 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_63.0-1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libamd-comgr3_7.0.2+dfsg-3 libamd-smi26_7.2.0-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.7-1 libasan8_16.1.0-1 libatomic1_16.1.0-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42.1-3 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_2.42-16 libc-dev-bin_2.42-16 libc-gconv-modules-extra_2.42-16 libc6_2.42-16 libc6-dev_2.42-16 libcap-ng0_0.9.3-1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-1 libclang-common-21-dev_1:21.1.8-7+b1 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl4t64_8.20.0-5 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_13.32 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-1 libdrm-common_2.4.134-1 libdrm-dev_2.4.134-1 libdrm-intel1_2.4.134-1 libdrm-nouveau2_2.4.134-1 libdrm-radeon1_2.4.134-1 libdrm2_2.4.134-1 libedit2_3.1-20260512-1 libeigen3-dev_3.4.0-5 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.1-1 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.2.0-17 libgcc-s1_16.1.0-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.2.0-17 libgfortran5_16.1.0-1 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_16.1.0-1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2.1 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-1 libhwloc-dev_2.14.0-1 libhwloc-plugins_2.14.0-1 libhwloc15_2.14.0-1 libibmad5_63.0-1 libibumad3_63.0-1 libibverbs-dev_63.0-1 libibverbs1_63.0-1 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-1 libjansson4_2.14-2+b4 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp26_1.9.7-2 libk5crypto3_1.22.1-2.1 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-2.1 libkrb5support0_1.22.1-2.1 libldap2_2.6.10+dfsg-1+b2 libllvm21_1:21.1.8-7+b1 liblocale-gettext-perl_1.07-10 liblsan0_16.1.0-1 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_2.42.1-3 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncl-dev_2.1.21+git20210811.b1213a7-6+b2 libncl2_2.1.21+git20210811.b1213a7-6+b2 libncursesw6_6.6+20251231-1+b1 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_1.7.0-5+b2 libpam-modules-bin_1.7.0-5+b2 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b2 libpciaccess-dev_0.17-3+b4 libpciaccess0_0.17-3+b4 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+b1 libproc2-0_2:4.0.4-9+b2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.21.5-1 libpsm2-2_11.2.185-2.1 libquadmath0_16.1.0-1 librdmacm1t64_63.0-1 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46-3 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.1-3 libsprng2_2.0a-19 libsprng2-dev_2.0a-19 libssh2-1t64_1.11.1-3 libssl3t64_3.6.2-1 libstdc++-15-dev_15.2.0-17 libstdc++6_16.1.0-1 libsystemd-shared_261~rc3-1 libsystemd0_261~rc3-1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-1 libubsan1_16.1.0-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b2 libucx0_1.20.1-1 libudev1_261~rc3-1 libunistring5_1.4.2-1 libuuid1_2.42.1-3 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_0.8.0+dfsg-9+b1 libyaml-cpp0.8_0.8.0+dfsg-9+b1 libz3-4_4.13.3-1.1 libze1_1.28.2-2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.10-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42.1-3 mpi-default-dev_1.20 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.3p1-4 openssl-provider-legacy_3.6.2-1 patch_2.8-2 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_2:4.0.4-9+b2 rpcsvc-proto_1.4.4-1 sed_4.9-3 sensible-utils_0.0.26 systemd_261~rc3-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 time_1.10-0.1 util-linux_2.42.1-3 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 Fri, 12 Jun 2026 09:55:14 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree3 Binary: iqtree3 Architecture: amd64 arm64 Version: 3.1.1+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/iqtree3 Vcs-Git: https://salsa.debian.org/med-team/iqtree3.git Testsuite: autopkgtest Testsuite-Triggers: time Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree3 deb science optional arch=amd64,arm64 Checksums-Sha1: 5cb91218fe0eb28acb346c2314a279e169827bc1 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz c1d9d2733c5e5f6b73fd651d1caf0bd56d343822 24212 iqtree3_3.1.1+dfsg-2.debian.tar.xz Checksums-Sha256: abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz 69c42c8624655fcbad54d233098f841c8f3bce130375c596d447f0a5b4356a13 24212 iqtree3_3.1.1+dfsg-2.debian.tar.xz Files: 8c195f00eb541abb6392e19f0d445e4f 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz 40337029245d0af522d540a800bbebdf 24212 iqtree3_3.1.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmoo78URHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE/FA/9GoLrs2uiFkYtvqlEGBnxZ8Mu3a0PB9Rj BxHqjUM1qLsCPDuZPqoR7W3uGvJQIB5d6Qw5wnuwZ/z6ELrDa/DeegiUMNcF+gn4 38YQZzJhpYRm6oGxtvm6VXBB9/zjeoN57l0pfkWWM/BzZSvowUcb4xYu0Mx8pXLg PUqvT+MPBNRD64zXpMD3mvsdZWglupdNV5JJv+NCl62NBVjFwSKoK/yTcB9uXdmq 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/usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting iqtree3 in /build/reproducible-path/iqtree3-3.1.1+dfsg dpkg-source: info: unpacking iqtree3_3.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree3_3.1.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake-4.patch dpkg-source: info: applying packaged-libs dpkg-source: info: applying no-baseline-violations dpkg-source: info: applying libeigen5.0.patch Check disk space ---------------- Sufficient free space for build 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=1781036498 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package iqtree3 dpkg-buildpackage: info: source version 3.1.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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:102 (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") -- 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 IQ-TREE flags : omp Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) 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 (1.2s) -- 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/iqtree3-3.1.1+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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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:102 (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") -- 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 IQ-TREE flags : Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) 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 (1.2s) -- 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/iqtree3-3.1.1+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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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:102 (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") -- 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 IQ-TREE flags : mpi Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 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 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) 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 (1.9s) -- 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/iqtree3-3.1.1+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp [ 2%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/bitset_index.c [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 3%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/alignment.c /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+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/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashmap.c [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/io.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/sort.c [ 4%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/booster.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c [ 6%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/prng.c [ 6%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/stats.c [ 7%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 7%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+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 ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+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/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/queue.c [ 14%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+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/recom.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+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/searchAlgo.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+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 CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/ssort.c [ 16%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/stack.c [ 16%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.c.o [ 17%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/trash.c cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+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/utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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) * | ^~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 18%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 18%] Built target pll make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp [ 21%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 24%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 24%] Built target nclextra make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/lcg64.c [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp [ 27%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/circularnetwork.cpp [ 27%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Built target lbfgsb [ 27%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/greedy.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 27%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen.c [ 28%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/gurobiwrapper.cpp [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/random.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 29%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/whtest.c /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/iqtree3-3.1.1+dfsg/build.omp' [ 30%] Built target kernelsse make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 30%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/vectorclass/instrset_detect.cpp [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 31%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp /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/iqtree3-3.1.1+dfsg/build.omp' [ 31%] Built target vectorclass make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 31%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp [ 33%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 33%] Built target gsl make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp [ 34%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 [ 34%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ /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/iqtree3-3.1.1+dfsg/build.omp' [ 34%] Built target lsd2 [ 35%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 36%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 36%] Built target whtest [ 36%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/split.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp [ 37%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~ [ 38%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Built target cmaple_utils make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp [ 38%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 38%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Built target pllavx [ 40%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitset.cpp [ 40%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 40%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/decenttree.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/iqtree3-3.1.1+dfsg/build.omp' [ 40%] Built target kernelfma [ 40%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopd.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp [ 42%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 42%] Built target phyloYAML [ 42%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/graph.cpp [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 43%] 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%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtree.cpp /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/iqtree3-3.1.1+dfsg/build.omp' [ 44%] Built target kernelavx [ 44%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 44%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/constraints.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 46%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/eigendecomposition.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/gzstream.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/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 47%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 48%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 48%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/optimization.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/iqtree3-3.1.1+dfsg/build.omp' [ 48%] Built target pda [ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/pllnni.cpp [ 52%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp [ 52%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 52%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp [ 54%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/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/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 54%] Built target decentTree [ 55%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 55%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 56%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp [ 57%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 58%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp [ 60%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/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/iqtree3-3.1.1+dfsg/build.omp' [ 60%] Built target terraphast In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 60%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/seqregionsmem.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/iqtree3-3.1.1+dfsg/build.omp' [ 60%] 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/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 62%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 62%] 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/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 63%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 63%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelbin.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldna.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 64%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactory.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelprotein.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelset.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelsubst.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategamma.cpp [ 66%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 66%] Built target cmaple_tree [ 67%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 67%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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) | ^~~~ [ 68%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 68%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 71%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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 -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratekategory.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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) | ^~~~ [ 71%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefree.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelcodon.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmixture.cpp tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 [ 73%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelunrest.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmm.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 75%] Built target cmaple [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 CMakeFiles/model.dir/modelcodonmixture.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorinvar.cpp [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/pattern.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtree.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/candidateset.cpp cd 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tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd 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/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd 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/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/ncbitree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd 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tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylosupertreeunlinked.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreepars.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreesse.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/quartet.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/supernode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/tinatree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/parstree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/discordance.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/phylosuperhmm.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/iqtree3-3.1.1+dfsg/build.omp' [ 93%] 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/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 93%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 93%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 94%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/presenceabsencematrix.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terrace.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 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main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/main.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/treetesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/timetree.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree3.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3 -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+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 -lyaml-cpp 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 -lyaml-cpp 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/iqtree3-3.1.1+dfsg/build.omp' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-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/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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 -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 0%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/bitset_index.c [ 0%] 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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp [ 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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 2%] 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_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+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 pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashmap.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/io.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/sort.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree.c [ 5%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/booster.c [ 5%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c [ 5%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/prng.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/stats.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+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%] Built target booster In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hash.c [ 8%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/lexer.c [ 8%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+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/genericParallelization.c.o In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/genericParallelization.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+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/optimizeModel.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+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/estimate_root.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp [ 11%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/queue.c [ 12%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+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/recom.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+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/searchAlgo.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+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/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/ssort.c [ 14%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/stack.c make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 14%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+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/treeIO.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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) * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 16%] Built target pll [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 17%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp [ 20%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp [ 25%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 25%] Built target nclextra make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 26%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 26%] Built target lsd2 [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/checkid.c make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Built target sprng make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/circularnetwork.cpp [ 27%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Built target ncl [ 27%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/greedy.cpp [ 27%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Built target lbfgsb [ 28%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/gurobiwrapper.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 28%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/vectorclass/instrset_detect.cpp [ 29%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 29%] Built target vectorclass [ 29%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 29%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp [ 30%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/random.c [ 31%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/whtest.c [ 32%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /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/iqtree3-3.1.1+dfsg/build.serial' [ 32%] Built target kernelsse make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 32%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp [ 33%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/split.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 34%] Built target gsl make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 36%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 36%] Built target whtest [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o [ 37%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 38%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c [ 38%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 40%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~ [ 40%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 40%] Built target cmaple_utils make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 40%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp [ 40%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 41%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.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/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp /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/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Built target kernelavx make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/decenttree.cpp [ 41%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Built target pllavx [ 41%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopd.cpp [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj.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/iqtree3-3.1.1+dfsg/build.serial' [ 42%] Built target kernelfma [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp [ 43%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 46%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 46%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 46%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 46%] Built target phyloYAML [ 47%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/graph.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 48%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtree.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/optimization.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 53%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 53%] Built target decentTree [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 54%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/pllnni.cpp [ 56%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/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/iqtree3-3.1.1+dfsg/build.serial' [ 56%] Built target pda [ 57%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 57%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp [ 57%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 [ 57%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/starttree.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/iqtree3-3.1.1+dfsg/build.serial' [ 57%] Built target terraphast [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/seqregionsmem.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/iqtree3-3.1.1+dfsg/build.serial' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/operatingsystem.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/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 62%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 62%] 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/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 63%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 63%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelbin.cpp [ 63%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldna.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactory.cpp [ 64%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 64%] Built target cmaple_tree make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 64%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelprotein.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelset.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelsubst.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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) | ^~~~ [ 66%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 66%] Built target maple make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 67%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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) | ^~~~ [ 68%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 68%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategamma.cpp tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 [ 70%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratekategory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefree.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelcodon.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmixture.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelunrest.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 74%] Built target cmaple [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmm.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 CMakeFiles/model.dir/modelcodonmixture.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 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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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/substitution.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignment.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/candidateset.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtreemix.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/matree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/memslot.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER 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/usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreepars.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd 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/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/supernode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd 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/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/phylosuperhmm.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o 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-I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terrace.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast && /usr/bin/cmake -P 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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/iqtree3-3.1.1+dfsg/build.serial' [ 95%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 95%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 95%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/main.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp [ 98%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.serial' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree3.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3 -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+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 -lyaml-cpp 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 -lyaml-cpp 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/iqtree3-3.1.1+dfsg/build.serial' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-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/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi 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'/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build [ 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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/bitset_index.c cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 2%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build /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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 2%] 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_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+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/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashmap.c [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/io.c [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/sort.c [ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c [ 4%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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 pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c [ 6%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/booster.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c [ 6%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/prng.c [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/stats.c [ 7%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 7%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+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 ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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 C object pll/CMakeFiles/pll.dir/genericParallelization.c.o [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/genericParallelization.c [ 13%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+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/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp [ 14%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+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/restartHashTable.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/stack.c [ 17%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+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/trash.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/treeIO.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+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/utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 20%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o [ 20%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp [ 24%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp [ 25%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 [ 25%] Linking CXX static library libncl.a /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 cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 [ 25%] Built target nclextra make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/lcg64.c /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/iqtree3-3.1.1+dfsg/build.mpi' [ 25%] Built target ncl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 25%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Built target sprng make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 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liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Built target lbfgsb [ 27%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen.c [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 28%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp [ 29%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/random.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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 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/build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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 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libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 30%] Built target kernelsse make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory 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-D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 32%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp [ 32%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 32%] Built target lsd2 make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi 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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 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/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 32%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/split.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 33%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp /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/iqtree3-3.1.1+dfsg/build.mpi' [ 34%] Built target whtest [ 34%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp [ 35%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp [ 35%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 35%] Built target gsl [ 36%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/splitset.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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 37%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 37%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 37%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopd.cpp [ 37%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/graph.cpp [ 38%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtree.cpp [ 38%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp [ 38%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp [ 40%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE 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/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp [ 40%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp [ 40%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake [ 40%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 40%] Built target cmaple_utils [ 40%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.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/iqtree3-3.1.1+dfsg/build.mpi' [ 40%] Built target kernelfma make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 41%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+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); | ^~~~~~~~~~~~~~~ make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/decenttree.cpp [ 42%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/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/iqtree3-3.1.1+dfsg/build.mpi' [ 42%] Built target pda make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils [ 43%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/starttree.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 44%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/eigendecomposition.cpp [ 44%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 44%] Built target pllavx make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 44%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 45%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 46%] 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 [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o [ 46%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/gzstream.cpp /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/iqtree3-3.1.1+dfsg/build.mpi' [ 46%] Built target kernelavx [ 46%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 46%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 46%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/optimization.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 47%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 [ 48%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.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/iqtree3-3.1.1+dfsg/build.mpi' [ 48%] Built target phyloYAML [ 48%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 50%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/gzstream.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 51%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/constraints.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 51%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/pllnni.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp [ 52%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/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/seqregionsmem.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/iqtree3-3.1.1+dfsg/build.mpi' [ 52%] 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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 52%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 54%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp [ 55%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 55%] Built target decentTree In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 55%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp [ 56%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 56%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp [ 56%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/bionj2.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/progress.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../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) | ^~~~ [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp [ 60%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 [ 61%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp "/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 CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 61%] 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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 61%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp [ 61%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp [ 62%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp [ 62%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp [ 63%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/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/iqtree3-3.1.1+dfsg/build.mpi' [ 63%] Built target terraphast In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/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) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 63%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp [ 63%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelbin.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldna.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactory.cpp [ 64%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 64%] Built target cmaple_tree [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelprotein.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelset.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelsubst.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 65%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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) | ^~~~ [ 67%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 67%] Built target maple [ 68%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 69%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -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/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../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) | ^~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 70%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratekategory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefree.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelcodon.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelmixture.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelunrest.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmm.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 76%] Built target cmaple [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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 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'/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 76%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 76%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 76%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/simulator/alisimulatorinvar.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/pattern.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 83%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/candidateset.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtreemix.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/memslot.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/ncbitree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/node.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/genomenode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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 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-I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylonode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylonodemixlen.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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 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cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylotreesse.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/quartet.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd 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/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/parstree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/discordance.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/phylosuperhmm.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/iqtree3-3.1.1+dfsg/build.mpi' [ 93%] 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/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 93%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 94%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/presenceabsencematrix.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/iqtree3-3.1.1+dfsg/terrace/terrace.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 95%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/main.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phylotesting.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/treetesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp [ 98%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.mpi' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree3.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: 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:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: 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:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3-mpi -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+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 -lyaml-cpp 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 -lyaml-cpp 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/iqtree3-3.1.1+dfsg/build.mpi' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp ... + /bin/time /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy IQ-TREE version 3.1.1 for Linux x86 64-bit built Jun 9 2026 Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy Seed: 555992 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Jun 12 10:08:09 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 Constructing alignment: done in 0.000356133 secs 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 4.1971e-05 secs 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) Checking for duplicate sequences: done in 7.5498e-05 secs 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: -11226.924 Optimal log-likelihood: -11226.901 Rate parameters: A-C: 1.42595 A-G: 2.32371 A-T: 1.71646 C-G: 1.90736 C-T: 2.78983 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.521 Parameters optimization took 1 rounds (0.016 sec) Time for fast ML tree search: 0.192 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 968 DNA models (sample size: 384 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 JC 11885.427 85 23940.855 23989.915 24276.659 2 JC+I 11632.742 86 23437.484 23487.868 23777.239 3 JC+G4 11316.936 86 22805.872 22856.256 23145.627 4 JC+I+G4 11301.274 87 22776.548 22828.277 23120.254 5 JC+R2 11410.712 87 22995.424 23047.154 23339.130 6 JC+R3 11309.803 89 22797.607 22852.097 23149.214 7 JC+R4 11297.894 91 22777.789 22835.131 23137.297 8 JC+R5 11297.411 93 22780.823 22841.112 23148.233 14 JC+I+R2 11342.644 88 22861.289 22914.387 23208.946 15 JC+I+R3 11300.043 90 22780.085 22835.990 23135.643 16 JC+I+R4 11296.757 92 22777.514 22836.318 23140.973 26 JC+I+G4 11301.274 87 22776.548 22828.277 23120.254 48 F81+I+G4 11301.275 87 22776.550 22828.279 23120.255 70 F81+F+I+G4 11297.145 90 22774.289 22830.193 23129.847 92 K2P+I+G4 11254.075 88 22684.149 22737.248 23031.806 114 K2P+I+G4 11254.075 88 22684.149 22737.248 23031.806 136 HKY+I+G4 11254.075 88 22684.149 22737.247 23031.806 158 HKY+F+I+G4 11247.176 91 22676.352 22733.695 23035.861 180 TNe+I+G4 11252.258 89 22682.516 22737.006 23034.123 202 TNe+I+G4 11252.258 89 22682.516 22737.006 23034.123 224 TN+I+G4 11252.257 89 22682.514 22737.004 23034.122 246 TN+F+I+G4 11244.583 92 22673.166 22731.970 23036.625 268 K3P+I+G4 11240.607 89 22659.214 22713.704 23010.821 290 K3P+I+G4 11240.607 89 22659.214 22713.704 23010.821 312 K3Pu+I+G4 11240.606 89 22659.211 22713.701 23010.819 334 K3Pu+F+I+G4 11234.507 92 22653.014 22711.818 23016.473 356 TPM2+I+G4 11254.065 89 22686.130 22740.620 23037.737 378 TPM2+I+G4 11254.065 89 22686.130 22740.620 23037.737 400 TPM2u+I+G4 11254.065 89 22686.129 22740.619 23037.736 422 TPM2u+F+I+G4 11247.113 92 22678.227 22737.031 23041.686 444 TPM3+I+G4 11246.664 89 22671.329 22725.818 23022.936 466 TPM3+I+G4 11246.664 89 22671.329 22725.818 23022.936 488 TPM3u+I+G4 11246.663 89 22671.327 22725.817 23022.934 510 TPM3u+F+I+G4 11243.496 92 22670.992 22729.796 23034.451 532 TIMe+I+G4 11238.866 90 22657.733 22713.637 23013.290 554 TIMe+I+G4 11238.866 90 22657.732 22713.637 23013.290 576 TIM+I+G4 11238.865 90 22657.731 22713.635 23013.288 598 TIM+F+I+G4 11232.015 93 22650.030 22710.320 23017.440 620 TIM2e+I+G4 11252.250 90 22684.501 22740.405 23040.058 642 TIM2e+I+G4 11252.250 90 22684.501 22740.405 23040.058 664 TIM2+I+G4 11252.250 90 22684.500 22740.404 23040.058 686 TIM2+F+I+G4 11244.529 93 22675.059 22735.349 23042.469 708 TIM3e+I+G4 11244.683 90 22669.366 22725.270 23024.924 730 TIM3e+I+G4 11244.683 90 22669.366 22725.270 23024.924 752 TIM3+I+G4 11244.682 90 22669.363 22725.268 23024.921 774 TIM3+F+I+G4 11240.828 93 22667.657 22727.946 23035.066 796 TVMe+I+G4 11231.964 91 22645.928 22703.270 23005.436 818 TVMe+I+G4 11231.964 91 22645.928 22703.270 23005.436 840 TVM+I+G4 11231.961 91 22645.922 22703.265 23005.431 862 TVM+F+I+G4 11229.463 94 22646.926 22708.726 23018.287 884 SYM+I+G4 11230.035 92 22644.070 22702.874 23007.529 906 SYM+I+G4 11230.035 92 22644.070 22702.874 23007.529 928 GTR+I+G4 11230.034 92 22644.067 22702.871 23007.526 950 GTR+F+I+G4 11226.901 95 22643.803 22707.136 23019.114 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+I+G4 Bayesian Information Criterion: TVM+I+G4 Best-fit model: TVM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 3.542 seconds (0h:0m:3s) Wall-clock time for ModelFinder: 3.574 seconds (0h:0m:3s) 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, 1.525 / Estimate: 0.000, 0.928 / LogL: -11244.232 Init pinv, alpha: 0.012, 1.525 / Estimate: 0.084, 1.518 / LogL: -11229.465 Init pinv, alpha: 0.023, 1.525 / Estimate: 0.084, 1.515 / LogL: -11229.465 Init pinv, alpha: 0.035, 1.525 / Estimate: 0.084, 1.514 / LogL: -11229.466 Init pinv, alpha: 0.046, 1.525 / Estimate: 0.084, 1.517 / LogL: -11229.465 Init pinv, alpha: 0.058, 1.525 / Estimate: 0.084, 1.514 / LogL: -11229.466 Init pinv, alpha: 0.069, 1.525 / Estimate: 0.084, 1.511 / LogL: -11229.471 Init pinv, alpha: 0.081, 1.525 / Estimate: 0.084, 1.515 / LogL: -11229.467 Init pinv, alpha: 0.093, 1.525 / Estimate: 0.085, 1.527 / LogL: -11229.463 Init pinv, alpha: 0.104, 1.525 / Estimate: 0.086, 1.533 / LogL: -11229.469 Optimal pinv,alpha: 0.085, 1.527 / LogL: -11229.463 Parameters optimization took 0.678 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00848482 secs using 99.99% CPU Computing ML distances took 0.008636 sec (of wall-clock time) 0.008598 sec (of CPU time) Setting up auxiliary I and S matrices: done in 7.9727e-05 secs using 100.3% CPU Constructing RapidNJ tree: done in 0.000194307 secs using 99.84% CPU Computing RapidNJ tree took 0.000378 sec (of wall-clock time) 0.000319 sec (of CPU time) Log-likelihood of RapidNJ tree: -11279.268 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.347 second Computing log-likelihood of 98 initial trees ... 0.426 seconds Current best score: -11229.463 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11229.424 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11222.888 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 3: -11222.397 Iteration 10 / LogL: -11222.510 / Time: 0h:0m:5s Iteration 20 / LogL: -11224.454 / Time: 0h:0m:6s Finish initializing candidate tree set (13) Current best tree score: -11222.397 / CPU time: 2.150 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11226.293 / Time: 0h:0m:7s (0h:0m:9s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 32: -11222.135 Iteration 40 / LogL: -11222.808 / Time: 0h:0m:8s (0h:0m:10s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 42: -11219.682 Iteration 50 / LogL: -11222.541 / Time: 0h:0m:9s (0h:0m:10s left) Iteration 60 / LogL: -11222.956 / Time: 0h:0m:9s (0h:0m:8s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 63: -11219.093 Iteration 70 / LogL: -11219.440 / Time: 0h:0m:10s (0h:0m:9s left) Iteration 80 / LogL: -11233.055 / Time: 0h:0m:11s (0h:0m:8s left) Iteration 90 / LogL: -11220.709 / Time: 0h:0m:12s (0h:0m:7s left) Iteration 100 / LogL: -11219.608 / Time: 0h:0m:13s (0h:0m:6s left) Iteration 110 / LogL: -11230.609 / Time: 0h:0m:14s (0h:0m:5s left) Iteration 120 / LogL: -11219.206 / Time: 0h:0m:15s (0h:0m:4s left) Iteration 130 / LogL: -11219.389 / Time: 0h:0m:15s (0h:0m:3s left) Iteration 140 / LogL: -11219.136 / Time: 0h:0m:16s (0h:0m:2s left) Iteration 150 / LogL: -11219.390 / Time: 0h:0m:17s (0h:0m:1s left) Iteration 160 / LogL: -11219.376 / Time: 0h:0m:18s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 164 ITERATIONS / Time: 0h:0m:18s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11219.093 Optimal log-likelihood: -11219.093 Rate parameters: A-C: 1.40787 A-G: 2.52211 A-T: 1.66882 C-G: 1.80874 C-T: 2.52211 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: 1.490 Parameters optimization took 1 rounds (0.015 sec) BEST SCORE FOUND : -11219.093 Total tree length: 12.887 Total number of iterations: 164 CPU time used for tree search: 14.132 sec (0h:0m:14s) Wall-clock time used for tree search: 14.452 sec (0h:0m:14s) Total CPU time used: 18.399 sec (0h:0m:18s) Total wall-clock time used: 18.760 sec (0h:0m:18s) 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: Fri Jun 12 10:08:28 2026 18.40user 0.33system 0:18.77elapsed 99%CPU (0avgtext+0avgdata 19132maxresident)k 0inputs+264outputs (0major+2689minor)pagefaults 0swaps + time /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo IQ-TREE version 3.1.1 for Linux x86 64-bit built Jun 9 2026 Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo Seed: 329746 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Jun 12 10:08:28 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 Constructing alignment: done in 0.000370719 secs using 94.95% CPU 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 5.2654e-05 secs using 81.67% 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) Checking for duplicate sequences: done in 8.5843e-05 secs using 88.53% CPU 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: -11222.570 Optimal log-likelihood: -11222.453 Rate parameters: A-C: 1.48105 A-G: 2.35929 A-T: 1.79126 C-G: 1.92551 C-T: 2.87198 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.531 Parameters optimization took 1 rounds (0.017 sec) Time for fast ML tree search: 0.177 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 968 DNA models (sample size: 384 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 JC 11882.518 85 23935.036 23984.096 24270.840 2 JC+I 11629.418 86 23430.836 23481.220 23770.592 3 JC+G4 11314.157 86 22800.315 22850.699 23140.070 4 JC+I+G4 11298.377 87 22770.754 22822.484 23114.460 5 JC+R2 11407.790 87 22989.579 23041.309 23333.285 6 JC+R3 11307.458 89 22792.916 22847.405 23144.523 7 JC+R4 11294.918 91 22771.837 22829.179 23131.345 8 JC+R5 11294.461 93 22774.921 22835.211 23142.331 14 JC+I+R2 11338.170 88 22852.340 22905.438 23199.997 15 JC+I+R3 11296.906 90 22773.812 22829.717 23129.370 16 JC+I+R4 11293.177 92 22770.355 22829.159 23133.814 26 JC+I+G4 11298.377 87 22770.754 22822.484 23114.460 48 F81+I+G4 11298.379 87 22770.757 22822.487 23114.463 70 F81+F+I+G4 11294.361 90 22768.721 22824.625 23124.279 92 K2P+I+G4 11251.082 88 22678.164 22731.262 23025.820 114 K2P+I+G4 11251.082 88 22678.164 22731.262 23025.820 136 HKY+I+G4 11251.082 88 22678.163 22731.262 23025.820 158 HKY+F+I+G4 11244.290 91 22670.580 22727.922 23030.088 180 TNe+I+G4 11248.857 89 22675.715 22730.204 23027.322 202 TNe+I+G4 11248.857 89 22675.715 22730.204 23027.322 224 TN+I+G4 11248.856 89 22675.712 22730.202 23027.319 246 TN+F+I+G4 11241.230 92 22666.460 22725.264 23029.919 268 K3P+I+G4 11237.659 89 22653.318 22707.808 23004.925 290 K3P+I+G4 11237.659 89 22653.318 22707.808 23004.925 312 K3Pu+I+G4 11237.658 89 22653.317 22707.806 23004.924 334 K3Pu+F+I+G4 11231.608 92 22647.215 22706.019 23010.674 356 TPM2+I+G4 11250.860 89 22679.720 22734.210 23031.327 378 TPM2+I+G4 11250.860 89 22679.720 22734.210 23031.327 400 TPM2u+I+G4 11250.859 89 22679.719 22734.209 23031.326 422 TPM2u+F+I+G4 11243.907 92 22671.814 22730.618 23035.273 444 TPM3+I+G4 11243.400 89 22664.799 22719.289 23016.406 466 TPM3+I+G4 11243.400 89 22664.799 22719.289 23016.406 488 TPM3u+I+G4 11243.398 89 22664.797 22719.286 23016.404 510 TPM3u+F+I+G4 11240.437 92 22664.874 22723.678 23028.333 532 TIMe+I+G4 11235.523 90 22651.046 22706.950 23006.604 554 TIMe+I+G4 11235.523 90 22651.046 22706.950 23006.604 576 TIM+I+G4 11235.522 90 22651.043 22706.948 23006.601 598 TIM+F+I+G4 11228.662 93 22643.323 22703.613 23010.733 620 TIM2e+I+G4 11248.650 90 22677.300 22733.205 23032.858 642 TIM2e+I+G4 11248.650 90 22677.300 22733.205 23032.858 664 TIM2+I+G4 11248.650 90 22677.300 22733.204 23032.857 686 TIM2+F+I+G4 11240.874 93 22667.747 22728.037 23035.157 708 TIM3e+I+G4 11240.996 90 22661.991 22717.895 23017.549 730 TIM3e+I+G4 11240.996 90 22661.991 22717.895 23017.549 752 TIM3+I+G4 11240.993 90 22661.987 22717.891 23017.545 774 TIM3+F+I+G4 11237.297 93 22660.595 22720.884 23028.004 796 TVMe+I+G4 11227.874 91 22637.749 22695.091 22997.257 818 TVMe+I+G4 11227.874 91 22637.749 22695.091 22997.257 840 TVM+I+G4 11227.872 91 22637.744 22695.086 22997.252 862 TVM+F+I+G4 11225.428 94 22638.857 22700.656 23010.217 884 SYM+I+G4 11225.569 92 22635.137 22693.942 22998.597 906 SYM+I+G4 11225.569 92 22635.137 22693.942 22998.596 928 GTR+I+G4 11225.567 92 22635.133 22693.938 22998.593 950 GTR+F+I+G4 11222.439 95 22634.878 22698.212 23010.189 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+I+G4 Bayesian Information Criterion: TVM+I+G4 Best-fit model: TVM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 3.528 seconds (0h:0m:3s) Wall-clock time for ModelFinder: 3.570 seconds (0h:0m:3s) 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, 1.537 / Estimate: 0.000, 0.935 / LogL: -11240.340 Init pinv, alpha: 0.012, 1.537 / Estimate: 0.085, 1.529 / LogL: -11225.427 Init pinv, alpha: 0.023, 1.537 / Estimate: 0.084, 1.527 / LogL: -11225.428 Init pinv, alpha: 0.035, 1.537 / Estimate: 0.084, 1.525 / LogL: -11225.429 Init pinv, alpha: 0.046, 1.537 / Estimate: 0.084, 1.528 / LogL: -11225.428 Init pinv, alpha: 0.058, 1.537 / Estimate: 0.084, 1.526 / LogL: -11225.430 Init pinv, alpha: 0.069, 1.537 / Estimate: 0.084, 1.522 / LogL: -11225.434 Init pinv, alpha: 0.081, 1.537 / Estimate: 0.084, 1.526 / LogL: -11225.431 Init pinv, alpha: 0.093, 1.537 / Estimate: 0.085, 1.538 / LogL: -11225.426 Init pinv, alpha: 0.104, 1.537 / Estimate: 0.086, 1.544 / LogL: -11225.431 Optimal pinv,alpha: 0.085, 1.538 / LogL: -11225.426 Parameters optimization took 0.649 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00845713 secs using 77.95% CPU Computing ML distances took 0.008668 sec (of wall-clock time) 0.006702 sec (of CPU time) Setting up auxiliary I and S matrices: done in 8.0198e-05 secs Constructing RapidNJ tree: done in 0.000211302 secs Computing RapidNJ tree took 0.000407 sec (of wall-clock time) 0.000000 sec (of CPU time) Log-likelihood of RapidNJ tree: -11279.095 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.343 second Computing log-likelihood of 98 initial trees ... 0.426 seconds Current best score: -11225.426 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11224.331 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11222.409 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 3: -11219.095 Iteration 10 / LogL: -11229.314 / Time: 0h:0m:5s Iteration 20 / LogL: -11222.947 / Time: 0h:0m:6s Finish initializing candidate tree set (15) Current best tree score: -11219.095 / CPU time: 2.107 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11219.180 / Time: 0h:0m:7s (0h:0m:9s left) Iteration 40 / LogL: -11219.707 / Time: 0h:0m:8s (0h:0m:7s left) Iteration 50 / LogL: -11219.097 / Time: 0h:0m:8s (0h:0m:5s left) Iteration 60 / LogL: -11219.170 / Time: 0h:0m:9s (0h:0m:4s left) Iteration 70 / LogL: -11219.407 / Time: 0h:0m:10s (0h:0m:3s left) Iteration 80 / LogL: -11229.451 / Time: 0h:0m:11s (0h:0m:2s left) Iteration 90 / LogL: -11219.152 / Time: 0h:0m:12s (0h:0m:1s left) Iteration 100 / LogL: -11219.348 / Time: 0h:0m:13s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 104 ITERATIONS / Time: 0h:0m:13s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11219.095 Optimal log-likelihood: -11219.093 Rate parameters: A-C: 1.41350 A-G: 2.53497 A-T: 1.67859 C-G: 1.81741 C-T: 2.53497 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: 1.488 Parameters optimization took 1 rounds (0.016 sec) BEST SCORE FOUND : -11219.093 Total tree length: 12.882 Total number of iterations: 104 CPU time used for tree search: 9.005 sec (0h:0m:9s) Wall-clock time used for tree search: 9.221 sec (0h:0m:9s) Total CPU time used: 13.231 sec (0h:0m:13s) Total wall-clock time used: 13.497 sec (0h:0m:13s) 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: Fri Jun 12 10:08:41 2026 13.24user 0.24system 0:13.51elapsed 99%CPU (0avgtext+0avgdata 18352maxresident)k 0inputs+248outputs (0major+2616minor)pagefaults 0swaps + rm -rf /tmp/iqtree3-test.8Qnfqn 31.65user 0.60system 0:32.32elapsed 99%CPU (0avgtext+0avgdata 19132maxresident)k 0inputs+560outputs (0major+6995minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1\+dfsg/debian/iqtree3 AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3" to "" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./models.nex -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.phy -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.nex -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j6 install DESTDIR=/build/reproducible-path/iqtree3-3.1.1\+dfsg/debian/iqtree3 AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi" to "" -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./models.nex -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.phy -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.nex -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_install find debian -name iqtree3-mpi -exec chrpath --delete \{\} \; find debian -name iqtree3-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree3 -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/iqtree3-3.1.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' mkdir -p /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3 > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-omp > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3-mpi.1 make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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 'iqtree3' in '../iqtree3_3.1.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'iqtree3-dbgsym' in '../iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree3_3.1.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree3_3.1.1+dfsg-2_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 2026-06-12T10:10:44Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Fri, 12 Jun 2026 10:10:45 +0000 | +------------------------------------------------------------------------------+ iqtree3_3.1.1+dfsg-2_amd64.changes: ----------------------------------- Format: 1.8 Date: Tue, 09 Jun 2026 22:21:38 +0200 Source: iqtree3 Binary: iqtree3 iqtree3-dbgsym Architecture: amd64 Version: 3.1.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: iqtree3 - efficient phylogenetic software by maximum likelihood; v3 Closes: 1136241 Changes: iqtree3 (3.1.1+dfsg-2) unstable; urgency=medium . * Build using Libeigen 5.0 Closes: #1136241 * d/watch: Use auto for Dversion-Mangle Checksums-Sha1: c1e07458f82ccece247ab7eb6a5a98bfb3d3ba54 122156284 iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb 73cfd9a0304ed5392b229f7ab4f5f20b276946c9 8738 iqtree3_3.1.1+dfsg-2_amd64.buildinfo ff4c363ec8ccc1ebfc06de58040d555574803f87 10723160 iqtree3_3.1.1+dfsg-2_amd64.deb Checksums-Sha256: 7193dfcfc7e11482ef01ac363eb8c46b95583ba2480cd196fadd33f89af1c715 122156284 iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb 0550073f7eddcdf02227852f25525da1ac329a020d9f917a08662c8c278d37d4 8738 iqtree3_3.1.1+dfsg-2_amd64.buildinfo 5acce2e38a90dfc628829fa781e1786144409a4eef2e13246693422e820a488a 10723160 iqtree3_3.1.1+dfsg-2_amd64.deb Files: 6ee6f754f1685575770960faafb18847 122156284 debug optional iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb 530abf27475650fdc8dd6be70919fea2 8738 science optional iqtree3_3.1.1+dfsg-2_amd64.buildinfo 38d3b8b5e41b185afaa9fa4a09832ce4 10723160 science optional iqtree3_3.1.1+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Fri, 12 Jun 2026 10:10:45 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree3 Binary: iqtree3 iqtree3-dbgsym Architecture: amd64 Version: 3.1.1+dfsg-2 Checksums-Md5: 6ee6f754f1685575770960faafb18847 122156284 iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb 38d3b8b5e41b185afaa9fa4a09832ce4 10723160 iqtree3_3.1.1+dfsg-2_amd64.deb Checksums-Sha1: c1e07458f82ccece247ab7eb6a5a98bfb3d3ba54 122156284 iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb ff4c363ec8ccc1ebfc06de58040d555574803f87 10723160 iqtree3_3.1.1+dfsg-2_amd64.deb Checksums-Sha256: 7193dfcfc7e11482ef01ac363eb8c46b95583ba2480cd196fadd33f89af1c715 122156284 iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb 5acce2e38a90dfc628829fa781e1786144409a4eef2e13246693422e820a488a 10723160 iqtree3_3.1.1+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 12 Jun 2026 10:10:43 +0000 Build-Path: /build/reproducible-path/iqtree3-3.1.1+dfsg Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 0.26-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.42.1-3), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), chrpath (= 0.18-1), cmake (= 4.3.3-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.2.0-17), cpp-15-x86-64-linux-gnu (= 15.2.0-17), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.32), 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 (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.2.0-17), g++-15-x86-64-linux-gnu (= 15.2.0-17), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.2.0-17), gcc-15-base (= 15.2.0-17), gcc-15-x86-64-linux-gnu (= 15.2.0-17), gcc-16-base (= 16.1.0-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 0.26-1), gettext-base (= 0.26-1), gfortran-15 (= 15.2.0-17), gfortran-15-x86-64-linux-gnu (= 15.2.0-17), 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 (= 63.0-1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libamd-comgr3 (= 7.0.2+dfsg-3), libamd-smi26 (= 7.2.0-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.7-1), libasan8 (= 16.1.0-1), libatomic1 (= 16.1.0-1), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-3), libblkid1 (= 2.42.1-3), 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 (= 2.42-16), libc-dev-bin (= 2.42-16), libc-gconv-modules-extra (= 2.42-16), libc6 (= 2.42-16), libc6-dev (= 2.42-16), libcap-ng0 (= 0.9.3-1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-1), libclang-common-21-dev (= 1:21.1.8-7+b1), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl4t64 (= 8.20.0-5), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 13.32), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-1), libdrm-common (= 2.4.134-1), libdrm-dev (= 2.4.134-1), libdrm-intel1 (= 2.4.134-1), libdrm-nouveau2 (= 2.4.134-1), libdrm-radeon1 (= 2.4.134-1), libdrm2 (= 2.4.134-1), libedit2 (= 3.1-20260512-1), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-dev (= 2.1.12-stable-10+b2), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b2), libexpat1 (= 2.8.1-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.5.2-4), libfido2-1 (= 1.17.0-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.2-2), libgcc-15-dev (= 15.2.0-17), libgcc-s1 (= 16.1.0-1), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-15-dev (= 15.2.0-17), libgfortran5 (= 16.1.0-1), 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 (= 16.1.0-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2.1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16.1.0-1), libhwloc-dev (= 2.14.0-1), libhwloc-plugins (= 2.14.0-1), libhwloc15 (= 2.14.0-1), libibmad5 (= 63.0-1), libibumad3 (= 63.0-1), libibverbs-dev (= 63.0-1), libibverbs1 (= 63.0-1), libidn2-0 (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-1), libjansson4 (= 2.14-2+b4), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp26 (= 1.9.7-2), libk5crypto3 (= 1.22.1-2.1), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-2.1), libkrb5support0 (= 1.22.1-2.1), libldap2 (= 2.6.10+dfsg-1+b2), libllvm21 (= 1:21.1.8-7+b1), liblocale-gettext-perl (= 1.07-10), liblsan0 (= 16.1.0-1), 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 (= 2.42.1-3), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncl-dev (= 2.1.21+git20210811.b1213a7-6+b2), libncl2 (= 2.1.21+git20210811.b1213a7-6+b2), libncursesw6 (= 6.6+20251231-1+b1), 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 (= 1.7.0-5+b2), libpam-modules-bin (= 1.7.0-5+b2), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b2), libpciaccess-dev (= 0.17-3+b4), libpciaccess0 (= 0.17-3+b4), 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+b1), libproc2-0 (= 2:4.0.4-9+b2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.21.5-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16.1.0-1), librdmacm1t64 (= 63.0-1), librhash1 (= 1.4.6-1.1+b1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46-3), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.1-3), libsprng2 (= 2.0a-19), libsprng2-dev (= 2.0a-19), libssh2-1t64 (= 1.11.1-3), libssl3t64 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-17), libstdc++6 (= 16.1.0-1), libsystemd-shared (= 261~rc3-1), libsystemd0 (= 261~rc3-1), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-1), libubsan1 (= 16.1.0-1), libucc1 (= 1.7.0~rc1-1), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.20.1-1), libudev1 (= 261~rc3-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.1-3), 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 (= 0.8.0+dfsg-9+b1), libyaml-cpp0.8 (= 0.8.0+dfsg-9+b1), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.10-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.42.1-3), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.3p1-4), openssl-provider-legacy (= 3.6.2-1), patch (= 2.8-2), 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 (= 2:4.0.4-9+b2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261~rc3-1), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.10-0.1), util-linux (= 2.42.1-3), 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="1781036498" +------------------------------------------------------------------------------+ | Package contents Fri, 12 Jun 2026 10:10:45 +0000 | +------------------------------------------------------------------------------+ iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb ------------------------------------- new Debian package, version 2.0. size 122156284 bytes: control archive=696 bytes. 465 bytes, 12 lines control 402 bytes, 4 lines md5sums Package: iqtree3-dbgsym Source: iqtree3 Version: 3.1.1+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 129256 Depends: iqtree3 (= 3.1.1+dfsg-2) Section: debug Priority: optional Description: debug symbols for iqtree3 Build-Ids: 2b0033214c7a4f9fe4d656ec85820af8377b8da1 9f41fd6255edf93a7d9045ec33faea0e1b294325 bd0613b9e913ed02edb07466c6bb6fc9b8fa234d drwxr-xr-x root/root 0 2026-06-09 20:21 ./ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.build-id/2b/ -rw-r--r-- root/root 38660048 2026-06-09 20:21 ./usr/lib/debug/.build-id/2b/0033214c7a4f9fe4d656ec85820af8377b8da1.debug drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.build-id/9f/ -rw-r--r-- root/root 38256816 2026-06-09 20:21 ./usr/lib/debug/.build-id/9f/41fd6255edf93a7d9045ec33faea0e1b294325.debug drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.build-id/bd/ -rw-r--r-- root/root 38256728 2026-06-09 20:21 ./usr/lib/debug/.build-id/bd/0613b9e913ed02edb07466c6bb6fc9b8fa234d.debug drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 17167768 2026-06-09 20:21 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree3.debug drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-06-09 20:21 ./usr/share/doc/iqtree3-dbgsym -> iqtree3 iqtree3_3.1.1+dfsg-2_amd64.deb ------------------------------ new Debian package, version 2.0. size 10723160 bytes: control archive=2352 bytes. 3212 bytes, 60 lines control 1114 bytes, 16 lines md5sums Package: iqtree3 Version: 3.1.1+dfsg-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 36226 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.8 (>= 0.7.0), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://www.iqtree.org Description: efficient phylogenetic software by maximum likelihood; v3 The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. . As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL. . Key features of IQ-TREE . - Efficient search algorithm: Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (Nguyen et al., 2015). - Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values (Minh et al., 2013). - Accurate model selection: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder (Kalyaanamoorthy et al., 2017). - Alignment simulation: A flexible simulator (AliSim) which allows to simulate sequence alignments under more realistic models than Seq-Gen and INDELible (Ly-Trong et al., 2023). - Phylogenetic testing: Several fast branch tests like SH-aLRT and aBayes test (Anisimova et al., 2011) and tree topology tests like the approximately unbiased (AU) test (Shimodaira, 2002). . The strength of IQ-TREE is the availability of a wide variety of phylogenetic models: . - Common models: All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites and ascertainment bias correction for e.g. SNP data. - Partition models: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions. - Mixture Models: fully customizable mixture models and empirical protein mixture models and. - Polymorphism-aware models (PoMo) http://www.iqtree.org/doc/Polymorphism-Aware-Models drwxr-xr-x root/root 0 2026-06-09 20:21 ./ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/bin/ -rwxr-xr-x root/root 11517272 2026-06-09 20:21 ./usr/bin/iqtree3 -rwxr-xr-x root/root 11611480 2026-06-09 20:21 ./usr/bin/iqtree3-mpi -rwxr-xr-x root/root 11517272 2026-06-09 20:21 ./usr/bin/iqtree3-omp drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/doc/iqtree3/ -rw-r--r-- root/root 278 2026-06-09 20:21 ./usr/share/doc/iqtree3/README.test -rw-r--r-- root/root 987 2026-06-09 20:21 ./usr/share/doc/iqtree3/changelog.Debian.gz -rw-r--r-- root/root 9858 2026-06-09 20:21 ./usr/share/doc/iqtree3/copyright drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/doc/iqtree3/examples/ -rw-r--r-- root/root 939 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/custom_distributions.txt -rw-r--r-- root/root 2237314 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.cf -rw-r--r-- root/root 174 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.nex -rw-r--r-- root/root 34178 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.phy -rw-r--r-- root/root 121669 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/models.nex -rw-r--r-- root/root 47 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/tree.nwk -rw-r--r-- root/root 2371 2026-06-09 20:21 ./usr/share/doc/iqtree3/run-unit-test drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/man/ drwxr-xr-x root/root 0 2026-06-09 20:21 ./usr/share/man/man1/ -rw-r--r-- root/root 7296 2026-06-09 20:21 ./usr/share/man/man1/iqtree3-mpi.1.gz -rw-r--r-- root/root 7274 2026-06-09 20:21 ./usr/share/man/man1/iqtree3-omp.1.gz -rw-r--r-- root/root 7254 2026-06-09 20:21 ./usr/share/man/man1/iqtree3.1.gz +------------------------------------------------------------------------------+ | Post Build Fri, 12 Jun 2026 10:10:47 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Fri, 12 Jun 2026 10:10:47 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Fri, 12 Jun 2026 10:10:49 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3518708 Build-Time: 929 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdzhXbrN/inputs/iqtree3_3.1.1+dfsg-2.dsc Machine Architecture: amd64 Package: iqtree3 Package-Time: 939 Source-Version: 3.1.1+dfsg-2 Space: 3518708 Status: successful Version: 3.1.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 2026-06-12T10:10:44Z Build needed 00:15:39, 3518708k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdzhXbrN/out checking iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb: size differs for iqtree3-dbgsym_3.1.1+dfsg-2_amd64.deb