=============================================================================== 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/rebuilderdKT9Ddd/inputs/iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo Source: iqtree3 Version: 3.1.1+dfsg-2 rebuilderd-worker node: osuosl42-amd64 +------------------------------------------------------------------------------+ | Downloading sources Tue, 21 Jul 2026 10:37:42 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [151 kB] Get:7 https://deb.debian.org/debian sid InRelease [193 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [185 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [1,840 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [89.5 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [276 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3,376 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [7,856 B] Get:18 https://deb.debian.org/debian forky/main Sources [11.1 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.8 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.8 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [391 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 35.1 MB in 4s (9,511 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 Tue, 21 Jul 2026 10:37:46 +0000 | +------------------------------------------------------------------------------+ Rebuilding iqtree3=3.1.1+dfsg-2 in /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdKT9Ddd/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs/iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs/iqtree3_3.1.1+dfsg-2+b1_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 [193 kB] Get:2 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable InRelease [193 kB] Get:3 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable InRelease [193 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages [10.6 MB] Get:5 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 Packages [10.6 MB] Get:6 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 Packages [10.6 MB] Fetched 32.4 MB in 3s (10.9 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260712T202631Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20260715T144045Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-8 [1677 kB] Fetched 1677 kB in 0s (95.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprwrptfqc/perl-base_5.40.1-8_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/tmpevv5i_b4/libbsd0_0.12.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzoil653d/m4_1.4.21-1_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/tmp6dr5_7u1/gcc_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Fetched 220 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe6pw8d0a/libnl-route-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42.2-2 [173 kB] Fetched 173 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvl3e94dm/libblkid1_2.42.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Fetched 31.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqswrhq0l/libkrb5support0_1.22.1-3_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/tmp02hawiha/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/tmpfpq4ehxv/libidn2-0_2.3.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42.2-2 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg392gap6/libsmartcols1_2.42.2-2_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 (177 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4hr4hrsm/libz3-4_4.13.3-1.1_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/tmpgv4a5tc1/gcc-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 261.1-3 [467 kB] Fetched 467 kB in 0s (45.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1zbbdkwj/libsystemd0_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.13-stable-1 [53.8 kB] Fetched 53.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6xj52u3j/libevent-pthreads-2.1-7t64_2.1.13-stable-1_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 (5942 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcw_mm_j/libncl-dev_2.1.21+git20210811.b1213a7-6+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/tmphqyymk7f/debianutils_5.23.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (4276 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaiguctug/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libubsan1 amd64 16.1.0-2 [1136 kB] Fetched 1136 kB in 0s (84.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qb4zkmh/libubsan1_16.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libctf0 amd64 2.46.50.20260617-1 [92.2 kB] Fetched 92.2 kB in 0s (1270 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsxk21mn1/libctf0_2.46.50.20260617-1_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/tmpaqqp7qog/libmagic1t64_5.47-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils amd64 2.46.50.20260617-1 [282 kB] Fetched 282 kB in 0s (5600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr079r0rj/binutils_2.46.50.20260617-1_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/tmpl4w0cwyu/libfuse3-4_3.18.2-2_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/tmpv8lgmtr8/libpsm2-2_11.2.185-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Fetched 3064 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqimia3z9/libboost-dev_1.90.0.2_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/tmpln3tzfd2/openmpi-common_5.0.10-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libucx0 amd64 1.22.0~rc1-1 [1015 kB] Fetched 1015 kB in 0s (71.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzpfvz29f/libucx0_1.22.0~rc1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Fetched 2658 kB in 0s (129 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppm14tosi/gettext_1.0-3_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 (956 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp88ech6i4/libsprng2-dev_2.0a-19_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b2 [670 kB] Fetched 670 kB in 0s (55.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3jaeh_0c/libpmix2t64_6.0.0+really5.0.9-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Fetched 13.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgx5cb8fd/chrpath_0.18-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libasan8 amd64 16.1.0-2 [2889 kB] Fetched 2889 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0uxn6dr2/libasan8_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-2 [166 kB] Fetched 166 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphefw7jgn/libhwloc15_2.14.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-2 [99.8 kB] Fetched 99.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpty8yyds8/bsdextrautils_2.42.2-2_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 (47.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu9ed2xlw/googletest_1.17.0-1_all.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 (82.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3c1akmg5/libopenmpi-dev_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 openssh-client amd64 1:10.4p1-1 [720 kB] Fetched 720 kB in 0s (8383 kB/s) dpkg-name: info: moved 'openssh-client_1%3a10.4p1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpwvby9gkt/openssh-client_10.4p1-1_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/tmpvoos_9nv/libcom-err2_1.47.4-1_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/tmpjshfod44/patch_2.8-2_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/tmp7vqh9r5w/libkeyutils1_1.6.3-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Fetched 77.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt8wwzhah/libdebhelper-perl_14.3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-3 [38.5 kB] Fetched 38.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptneqlq6m/libdrm2_2.4.134-3_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/tmpykqub53q/liblocale-gettext-perl_1.07-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.11-2 [87.3 kB] Fetched 87.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptghvn1q7/libselinux1_3.11-2_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/tmpm31du1ed/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.4-1 [16.2 MB] Fetched 16.2 MB in 0s (174 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx1yuion2/cmake_4.3.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libatomic1 amd64 16.1.0-2 [10.4 kB] Fetched 10.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp28roc1_l/libatomic1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.19-2 [18.5 kB] Fetched 18.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpowv3shcq/libpciaccess0_0.19-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-16-base amd64 16.1.0-2 [36.8 kB] Fetched 36.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfoh510ug/gcc-16-base_16.1.0-2_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/tmpw_3axsg1/libpipeline1_1.5.8-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46.50.20260617-1 [1077 kB] Fetched 1077 kB in 0s (6157 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fv1oq5_/binutils-x86-64-linux-gnu_2.46.50.20260617-1_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/tmpyik5h3hw/librhash1_1.4.6-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-3 [331 kB] Fetched 331 kB in 0s (32.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5pz64ria/sed_4.9-3_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/tmpruwyxaqv/libpkgconf7_2.5.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.3.0-1 [23.4 MB] Fetched 23.4 MB in 0s (183 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyxm1mvin/gcc-15-x86-64-linux-gnu_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.15.1-1 [65.6 kB] Fetched 65.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lt5zidy/libjansson4_2.15.1-1_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 (62.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn3dnek7/libxml2-16_2.15.3+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 libyaml-cpp-dev amd64 0.9.0+dfsg-5 [188 kB] Fetched 188 kB in 0s (4736 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgwgvdekv/libyaml-cpp-dev_0.9.0+dfsg-5_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/tmpkbz_g3o5/libsasl2-2_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-3 [1559 kB] Fetched 1559 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprtd3pq5e/bash_5.3-3_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 (54.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz0n0iy4v/libhsa-runtime64-1_6.4.3+dfsg-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/tmp3ixfu75k/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Fetched 183 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy_wmnfdc/libevent-2.1-7t64_2.1.13-stable-1_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/tmp55b7dadl/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b2 [27.1 kB] Fetched 27.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpztsq445y/libxxhash0_0.8.3-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 binutils-common amd64 2.46.50.20260617-1 [2636 kB] Fetched 2636 kB in 0s (33.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4fo8i6y_/binutils-common_2.46.50.20260617-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260715T144045Z unstable/main amd64 libyaml-cpp0.9 amd64 0.9.0+dfsg-5 [147 kB] Fetched 147 kB in 0s (2891 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2nklnenx/libyaml-cpp0.9_0.9.0+dfsg-5_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/tmpqbyafm0j/pkgconf-bin_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (128 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2s5xwwa_/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4xisx91t/libgssapi-krb5-2_1.22.1-3_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/tmpywt40ulg/libmagic-mgc_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-17 [620 kB] Fetched 620 kB in 0s (54.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpao5ijb2l/libc-bin_2.42-17_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/tmpj7pifbv4/file_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.8-2 [362 kB] Fetched 362 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphtjccse5/libarchive13t64_3.8.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-11 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpneihoaip/libltdl-dev_2.5.4-11_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 (154 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvzzhyloh/libperl5.40_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-17 [1097 kB] Fetched 1097 kB in 0s (84.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfuudr2j_/libc-gconv-modules-extra_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-2 [43.2 kB] Fetched 43.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppks9ywgt/libibmad5_63.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (2495 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4mrrs__1/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsprng2 amd64 2.0a-19 [76.0 kB] Fetched 76.0 kB in 0s (1410 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw_xdut6f/libsprng2_2.0a-19_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 (5006 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3o6mmw4c/libedit2_3.1-20260512-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB] Fetched 422 kB in 0s (7172 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyhykjaow/libcurl4t64_8.21.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (9207 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfl9rfydm/libarchive-zip-perl_1.68-1_all.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/tmpd4q88tff/libgdbm6t64_1.26-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Fetched 918 kB in 0s (67.5 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp2bbvynmq/zlib1g-dev_1.3.dfsg+really1.3.2-3_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 (30.4 MB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmps_co1lhd/libgmpxx4ldbl_6.3.0+dfsg-5+b2_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 (2017 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp004klua_/intltool-debian_0.35.0+20060710.6_all.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 (101 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv5ayloed/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp200ze69f/hostname_3.25_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 (8336 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5pkhbgcz/libnl-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Fetched 877 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgkp3xuta/libgfortran5_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.6.3-1 [2488 kB] Fetched 2488 kB in 0s (127 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv7tbtp6h/libssl3t64_3.6.3-1_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/tmp7b3815tu/mawk_1.3.4.20260302-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libsframe3 amd64 2.46.50.20260617-1 [84.7 kB] Fetched 84.7 kB in 0s (2589 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_4ppqry/libsframe3_2.46.50.20260617-1_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 (0 B/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmpouxgalp1/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 7.1.3-1 [1963 kB] Fetched 1963 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt95x_kfz/linux-libc-dev_7.1.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Fetched 516 kB in 0s (47.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgfzlp08b/autoconf_2.73-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42.2-2 [1230 kB] Fetched 1230 kB in 0s (92.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcevuz0b/util-linux_2.42.2-2_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 (120 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_5a859pn/libopenmpi40_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261.1-3 [2566 kB] Fetched 2566 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcss9cvx5/libsystemd-shared_261.1-3_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/tmp0xr6n6vf/libpcre2-8-0_10.46-1+b2_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 (69.1 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmpf3yxieao/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-3 [7860 B] Fetched 7860 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaefltgqi/libdrm-common_2.4.134-3_all.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/tmpscodi3vk/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4ngbfob/libfile-stripnondeterminism-perl_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Fetched 244 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3q71ehny/libssh2-1t64_1.11.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Fetched 154 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3h_0uq07/openmpi-bin_5.0.10-1_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/tmp2_2s1m4e/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20260608-2 [276 kB] Fetched 276 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm3ol11qe/ncurses-base_6.6+20260608-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (15.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt00plegm/libisl23_0.27-2_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/tmpg2hkw85k/bzip2_1.0.8-6+b2_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/tmpf_0q745a/pkg-config_2.5.1-4_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/tmp79a5en7p/po-debconf_1.0.22_all.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/tmpfuyqbhmh/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0h6n98xa/gettext-base_1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgcc-15-dev amd64 15.3.0-1 [2718 kB] Fetched 2718 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvautogq2/libgcc-15-dev_15.3.0-1_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 (42.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2pnse0qe/libprrte3_3.0.13-3_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 (8523 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpunb0o3df/libnghttp2-14_1.69.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libstdc++-15-dev amd64 15.3.0-1 [2784 kB] Fetched 2784 kB in 0s (135 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppljm3hdx/libstdc++-15-dev_15.3.0-1_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/tmpzo31bsoq/ocl-icd-libopencl1_2.3.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ffdtiw4/grep_3.12-1_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/tmpotw1s6om/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Fetched 121 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpotl1058u/libexpat1_2.8.2-1_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/tmpvbdcqzv9/build-essential_12.12_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 (61.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8xommex/libdpkg-perl_1.23.7_all.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/tmpm_axfoxg/mpi-default-dev_1.20_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 (66.8 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp4k0o4qze/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-17 [1991 kB] Fetched 1991 kB in 0s (117 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb6ewncy9/libc6-dev_2.42-17_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 (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzeaowdow/perl-modules-5.40_5.40.1-8_all.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/tmpc5lvd2lp/libxext6_1.3.4-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Fetched 79.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5u08nxu/libk5crypto3_1.22.1-3_amd64.deb' Downloading dependency 1 of 265: perl-base:amd64=5.40.1-8 Downloading dependency 2 of 265: libbsd0:amd64=0.12.2-3 Downloading dependency 3 of 265: m4:amd64=1.4.21-1 Downloading dependency 4 of 265: gcc:amd64=4:15.2.0-5+b1 Downloading dependency 5 of 265: libnl-route-3-dev:amd64=3.12.0-2+b1 Downloading dependency 6 of 265: libblkid1:amd64=2.42.2-2 Downloading dependency 7 of 265: libkrb5support0:amd64=1.22.1-3 Downloading dependency 8 of 265: gzip:amd64=1.13-1 Downloading dependency 9 of 265: libidn2-0:amd64=2.3.8-5 Downloading dependency 10 of 265: libsmartcols1:amd64=2.42.2-2 Downloading dependency 11 of 265: libz3-4:amd64=4.13.3-1.1 Downloading dependency 12 of 265: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 13 of 265: libsystemd0:amd64=261.1-3 Downloading dependency 14 of 265: libevent-pthreads-2.1-7t64:amd64=2.1.13-stable-1 Downloading dependency 15 of 265: libncl-dev:amd64=2.1.21+git20210811.b1213a7-6+b2 Downloading dependency 16 of 265: debianutils:amd64=5.23.2 Downloading dependency 17 of 265: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 18 of 265: libubsan1:amd64=16.1.0-2 Downloading dependency 19 of 265: libctf0:amd64=2.46.50.20260617-1 Downloading dependency 20 of 265: libmagic1t64:amd64=1:5.47-4 Downloading dependency 21 of 265: binutils:amd64=2.46.50.20260617-1 Downloading dependency 22 of 265: libfuse3-4:amd64=3.18.2-2 Downloading dependency 23 of 265: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 24 of 265: libboost-dev:amd64=1.90.0.2 Downloading dependency 25 of 265: openmpi-common:amd64=5.0.10-1 Downloading dependency 26 of 265: libucx0:amd64=1.22.0~rc1-1 Downloading dependency 27 of 265: gettext:amd64=1.0-3 Downloading dependency 28 of 265: libsprng2-dev:amd64=2.0a-19 Downloading dependency 29 of 265: libpmix2t64:amd64=6.0.0+really5.0.9-3+b2 Downloading dependency 30 of 265: chrpath:amd64=0.18-1 Downloading dependency 31 of 265: libasan8:amd64=16.1.0-2 Downloading dependency 32 of 265: libhwloc15:amd64=2.14.0-2 Downloading dependency 33 of 265: bsdextrautils:amd64=2.42.2-2 Downloading dependency 34 of 265: googletest:amd64=1.17.0-1 Downloading dependency 35 of 265: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 36 of 265: openssh-client:amd64=1:10.4p1-1 Downloading dependency 37 of 265: libcom-err2:amd64=1.47.4-1 Downloading dependency 38 of 265: patch:amd64=2.8-2 Downloading dependency 39 of 265: libkeyutils1:amd64=1.6.3-6+b2 Downloading dependency 40 of 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dependency 72 of 265: file:amd64=1:5.47-4 Downloading dependency 73 of 265: libarchive13t64:amd64=3.8.8-2 Downloading dependency 74 of 265: libltdl-dev:amd64=2.5.4-11 Downloading dependency 75 of 265: libperl5.40:amd64=5.40.1-8 Downloading dependency 76 of 265: libc-gconv-modules-extra:amd64=2.42-17 Downloading dependency 77 of 265: libibmad5:amd64=63.0-2 Downloading dependency 78 of 265: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 79 of 265: libsprng2:amd64=2.0a-19 Downloading dependency 80 of 265: libedit2:amd64=3.1-20260512-1 Downloading dependency 81 of 265: libcurl4t64:amd64=8.21.0-2 Downloading dependency 82 of 265: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 83 of 265: libgdbm6t64:amd64=1.26-1+b2 Downloading dependency 84 of 265: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 85 of 265: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 86 of 265: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 87 of 265: man-db:amd64=2.13.1-1 Downloading dependency 88 of 265: hostname:amd64=3.25 Downloading dependency 89 of 265: libnl-3-dev:amd64=3.12.0-2+b1 Downloading dependency 90 of 265: libgfortran5:amd64=16.1.0-2 Downloading dependency 91 of 265: libssl3t64:amd64=3.6.3-1 Downloading dependency 92 of 265: mawk:amd64=1.3.4.20260302-1 Downloading dependency 93 of 265: libsframe3:amd64=2.46.50.20260617-1 Downloading dependency 94 of 265: libx11-data:amd64=2:1.8.13-1 Downloading dependency 95 of 265: linux-libc-dev:amd64=7.1.3-1 Downloading dependency 96 of 265: autoconf:amd64=2.73-2 Downloading dependency 97 of 265: util-linux:amd64=2.42.2-2 Downloading dependency 98 of 265: libopenmpi40:amd64=5.0.10-1 Downloading dependency 99 of 265: libsystemd-shared:amd64=261.1-3 Downloading dependency 100 of 265: libpcre2-8-0:amd64=10.46-1+b2 Downloading dependency 101 of 265: automake:amd64=1:1.18.1-4 Downloading dependency 102 of 265: libdrm-common:amd64=2.4.134-3 Downloading dependency 103 of 265: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 104 of 265: libfile-stripnondeterminism-perl:amd64=1.15.1-1 Downloading dependency 105 of 265: libssh2-1t64:amd64=1.11.1-4 Downloading dependency 106 of 265: openmpi-bin:amd64=5.0.10-1 Downloading dependency 107 of 265: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 108 of 265: ncurses-base:amd64=6.6+20260608-2 Downloading dependency 109 of 265: libisl23:amd64=0.27-2 Downloading dependency 110 of 265: bzip2:amd64=1.0.8-6+b2 Downloading dependency 111 of 265: pkg-config:amd64=2.5.1-4 Downloading dependency 112 of 265: po-debconf:amd64=1.0.22 Downloading dependency 113 of 265: diffutils:amd64=1:3.12-1 Downloading dependency 114 of 265: gettext-base:amd64=1.0-3 Downloading dependency 115 of 265: libgcc-15-dev:amd64=15.3.0-1 Downloading dependency 116 of 265: libprrte3:amd64=3.0.13-3 Downloading dependency 117 of 265: libnghttp2-14:amd64=1.69.0-1 Downloading dependency 118 of 265: libstdc++-15-dev:amd64=15.3.0-1 Downloading dependency 119 of 265: ocl-icd-libopencl1:amd64=2.3.4-1+b1 Downloading dependency 120 of 265: grep:amd64=3.12-1 Downloading dependency 121 of 265: help2man:amd64=1.49.3 Downloading dependency 122 of 265: libexpat1:amd64=2.8.2-1 Downloading dependency 123 of 265: build-essential:amd64=12.12 Downloading dependency 124 of 265: libdpkg-perl:amd64=1.23.7 Downloading dependency 125 of 265: mpi-default-dev:amd64=1.20 Downloading dependency 126 of 265: libx11-6:amd64=2:1.8.13-1 Downloading dependency 127 of 265: libc6-dev:amd64=2.42-17 Downloading dependency 128 of 265: perl-modules-5.40:amd64=5.40.1-8 Downloading dependency 129 of 265: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 130 of 265: libk5crypto3:amd64=1.22.1-3 Downloading dependency 131 of 265: libtsan2:amd64=16.1.0-2Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libtsan2 amd64 16.1.0-2 [2573 kB] Fetched 2573 kB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5mps538j/libtsan2_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Fetched 13.9 MB in 0s (186 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqffapsk2/libamd-comgr3_7.0.2+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libcc1-0 amd64 16.1.0-2 [46.1 kB] Fetched 46.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpapgzvm78/libcc1-0_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Fetched 109 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqx45vrbz/dwz_0.17-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.52.1-4 [158 kB] Fetched 158 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbmxxc9aw/libuv1t64_1.52.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.4.0-1 [37.1 kB] Fetched 37.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpur7nmth0/libacl1_2.4.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Fetched 3654 kB in 0s (143 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0zsexgsn/libprrte-dev_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Fetched 335 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2y3086n8/libkrb5-3_1.22.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libctf-nobfd0 amd64 2.46.50.20260617-1 [160 kB] Fetched 160 kB in 0s (4284 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfw4nosk3/libctf-nobfd0_2.46.50.20260617-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.13+dfsg-1 [188 kB] Fetched 188 kB in 0s (18.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_0vsbggs/libldap2_2.6.13+dfsg-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/tmprek262jn/libprrte-bin_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (53.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgsqspqgz/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20260608-2 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplklvp2jf/libncursesw6_6.6+20260608-2_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/tmp7t8a6h9i/g++_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-8 [246 kB] Fetched 246 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphlky8o91/libpam-runtime_1.7.0-8_all.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 (23.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9mlyd6rx/libsimde-dev_0.8.4~rc3-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Fetched 480 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd10y8i4j/libunistring5_1.4.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.6-2 [983 kB] Fetched 983 kB in 0s (81.6 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.6-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpprz_2_uc/procps_4.0.6-2_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/tmp9vy2su9e/libxdmcp6_1.1.5-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.3.0-1 [12.8 MB] Fetched 12.8 MB in 0s (35.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppspp5ic8/gfortran-15-x86-64-linux-gnu_15.3.0-1_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 (2543 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3u2bkb8s/time_1.10-0.1_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/tmpv5pqgdfv/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Fetched 416 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnik10gp7/libltdl7_2.5.4-11_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/tmppcdw8a9z/libcrypt1_4.5.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Fetched 133 kB in 0s (405 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3muw0zs0/libngtcp2-16_1.22.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libhwasan0 amd64 16.1.0-2 [1580 kB] Fetched 1580 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvx9eofas/libhwasan0_16.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgomp1 amd64 16.1.0-2 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpivdxxo76/libgomp1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Fetched 934 kB in 0s (79.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwja61edy/debhelper_14.3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-17 [38.1 kB] Fetched 38.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdz03p342/libc-dev-bin_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.283 [7572 B] Fetched 7572 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3twipq72/libdebconfclient0_0.283_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 (65.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpusn__29s/libmpfr6_4.2.2-3_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 (11.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp7qpk7q2/libncl2_2.1.21+git20210811.b1213a7-6+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.13-stable-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfllb0psu/libevent-dev_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (60.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxpn2mq2f/dpkg-dev_1.23.7_all.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 (1777 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkalc6chr/libmunge2_0.5.18-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.3.0-1 [13.2 MB] Fetched 13.2 MB in 0s (188 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvzdtg5x2/g++-15-x86-64-linux-gnu_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-8 [66.9 kB] Fetched 66.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsmhxeah2/libpam0g_1.7.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-1 amd64 2:4.0.6-2 [69.2 kB] Fetched 69.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-1_2%3a4.0.6-2_amd64.deb' to '/srv/rebuilderd/tmp/tmp1ubgcd_z/libproc2-1_4.0.6-2_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/tmposdlc577/libnettle8t64_3.10.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15-base amd64 15.3.0-1 [37.4 kB] Fetched 37.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4o969wzo/gcc-15-base_15.3.0-1_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/tmpw9m6x0sm/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-4 [700 kB] Fetched 700 kB in 0s (65.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplt98ioq0/findutils_4.10.0-4_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/tmp81vh9qja/cpp_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pci.ids all 0.0~2026.07.06-1 [285 kB] Fetched 285 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw2r2ws9j/pci.ids_0.0~2026.07.06-1_all.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/tmpasat4_w_/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.4-1 [63.4 kB] Fetched 63.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_w200ymn/rpcsvc-proto_1.4.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.13-stable-1 [60.9 kB] Fetched 60.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj628o7_x/libevent-openssl-2.1-7t64_2.1.13-stable-1_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 (163 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpedy0tm4y/libamdhip64-6_6.4.3-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b4 [768 kB] Fetched 768 kB in 0s (61.4 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmphyf02ysh/libclang-common-21-dev_21.1.8-7+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-8 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1aam_w1x/libpam-modules_1.7.0-8_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 (83.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_1u1wed/libeigen3-dev_3.4.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.3-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb0m8qbj5/liblzma5_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 261.1-3 [139 kB] Fetched 139 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmporgjmc63/libudev1_261.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Fetched 820 kB in 0s (69.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmqr120iz/autopoint_1.0-3_all.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/tmp2zineptt/libxau6_1.0.11-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 cpp-15 amd64 15.3.0-1 [1280 B] Fetched 1280 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvzr0i6lj/cpp-15_15.3.0-1_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/tmp8xcbtsrn/base-files_14.2_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 (58.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy02oy29i/xz-utils_5.8.3-1_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 (60.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zgo7jb8/libze1_1.28.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgcc-s1 amd64 16.1.0-2 [74.1 kB] Fetched 74.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsf3j9sgd/libgcc-s1_16.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 liblsan0 amd64 16.1.0-2 [1281 kB] Fetched 1281 kB in 0s (95.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgyibve86/liblsan0_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.1-1 [49.9 kB] Fetched 49.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgbyv577/libseccomp2_2.6.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gcc-15 amd64 15.3.0-1 [546 kB] Fetched 546 kB in 0s (52.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfx7hukp5/gcc-15_15.3.0-1_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/tmpw90k7om5/perl_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (98.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjy0vpoor/dpkg_1.23.7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20260608-2 [353 kB] Fetched 353 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprosrogrc/libtinfo6_6.6+20260608-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libstdc++6 amd64 16.1.0-2 [822 kB] Fetched 822 kB in 0s (68.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_uudl1ri/libstdc++6_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (36.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptem0kn14/make_4.4.1-3_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 (1386 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpokgkqudd/libxnvctrl0_535.171.04-1+b3_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/tmpctgw3ws3/sysvinit-utils_3.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Fetched 716 kB in 0s (62.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_06r6jq0/libfabric1_2.1.0-1.1+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/tmp9z7tk2u8/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.6.0-1 [24.7 kB] Fetched 24.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.6.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpt4xxxren/libattr1_2.6.0-1_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 (7325 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuda0mq6r/libfido2-1_1.17.0-1_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/tmpbllqfsd3/libzstd1_1.5.7+dfsg-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-2 [383 kB] Fetched 383 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp15s680d1/ibverbs-providers_63.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 g++-15 amd64 15.3.0-1 [28.7 kB] Fetched 28.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm95orgsq/g++-15_15.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgfortran-15-dev amd64 15.3.0-1 [877 kB] Fetched 877 kB in 0s (23.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9korjw5f/libgfortran-15-dev_15.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libgprofng0 amd64 2.46.50.20260617-1 [821 kB] Fetched 821 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1gj4vt45/libgprofng0_2.46.50.20260617-1_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/tmps9po85bs/libmd0_1.2.0-2_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/tmp61mez64l/g++-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.13-stable-1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp01gl1c4e/libevent-core-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.13-stable-1 [108 kB] Fetched 108 kB in 0s (9582 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz0b6j8eq/libevent-extra-2.1-7t64_2.1.13-stable-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-2 [21.7 kB] Fetched 21.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcg3xp8az/libhwloc-plugins_2.14.0-2_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjtbjub5b/base-passwd_3.6.8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libbinutils amd64 2.46.50.20260617-1 [536 kB] Fetched 536 kB in 0s (3972 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_9t_5tq/libbinutils_2.46.50.20260617-1_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/tmpn77ivszo/libnl-3-200_3.12.0-2+b1_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/tmpmtip3hkr/libnl-route-3-200_3.12.0-2+b1_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/tmp5ggp7zdj/libnuma-dev_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.0-1 [60.8 kB] Fetched 60.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuz6v11ec/libpsl5t64_0.23.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-2 [71.8 kB] Fetched 71.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfmpktvhm/librdmacm1t64_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Fetched 22.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8g6pwd75/libnuma1_2.0.19-1+b2_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/tmpttrw9qkz/libcbor0.10_0.10.2-2.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-2 [260 kB] Fetched 260 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0kex3ys4/libhwloc-dev_2.14.0-2_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/tmpjtmmvcz7/zlib1g_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Fetched 320 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaljf5dm7/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptkhm2snw/init-system-helpers_1.69_all.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/tmperww5sf2/libelf1t64_0.195-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.7.1-2 [30.5 kB] Fetched 30.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodlkxbk_/libffi8_3.7.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-2 [695 kB] Fetched 695 kB in 0s (65.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp14t5lccp/libibverbs-dev_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-8 [46.3 kB] Fetched 46.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvva47ubh/libpam-modules-bin_1.7.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.8.0-2 [345 kB] Fetched 345 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmple7seyfw/libucc1_1.8.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-17 [1790 kB] Fetched 1790 kB in 0s (99.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssg8ig8e/libc6_2.42-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-10 [70.3 kB] Fetched 70.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp51129ev/liblz4-1_1.10.0-10_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/tmpnfdy78ex/libuchardet0_0.0.8-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [4644 B] Fetched 4644 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpq0s4yek0/cpp-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b2 [560 kB] Fetched 560 kB in 0s (51.8 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpr0igou4a/libgmp10_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20260608-2 [445 kB] Fetched 445 kB in 0s (43.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjoa3gw8/ncurses-bin_6.6+20260608-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 openssh-common amd64 1:10.4p1-1 [481 kB] Fetched 481 kB in 0s (10.0 MB/s) dpkg-name: info: moved 'openssh-common_1%3a10.4p1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxgnv5dth/openssh-common_10.4p1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.6.3-1 [320 kB] Fetched 320 kB in 0s (31.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpda8nnnhs/openssl-provider-legacy_3.6.3-1_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 (56.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6_deu0vv/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.8-2 [87.5 kB] Fetched 87.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu6ledksa/libjsoncpp26_1.9.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB] Fetched 23.3 kB in 0s (1031 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaclk0apw/libngtcp2-crypto-ossl0_1.22.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42.2-2 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplttcpynj/libuuid1_2.42.2-2_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/tmpqwg7z1o1/libgdbm-compat4t64_1.26-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.3.0-1 [12.1 MB] Fetched 12.1 MB in 0s (126 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprdwrfv2_/cpp-15-x86-64-linux-gnu_15.3.0-1_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/tmp5n_pe4s7/libbz2-1.0_1.0.8-6+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/tmpvcjfs6xf/libmpc3_1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk7a4mtbv/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42.2-2 [215 kB] Fetched 215 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_v99hpzc/libmount1_2.42.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.3-1+b1 [18.2 kB] Fetched 18.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8vmq_i18/libcap-ng0_0.9.3-1+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/tmpceoqcm8a/libsasl2-modules-db_2.1.28+dfsg1-11_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 (91.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8vkoi27/groff-base_1.24.1-1_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 (54.4 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp65ewhga1/libgmp-dev_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-2 [28.5 kB] Fetched 28.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1vmsoa6u/libibumad3_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-3 [23.3 kB] Fetched 23.3 kB in 0s (2028 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7hx6yl0f/libdrm-amdgpu1_2.4.134-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Fetched 11.3 MB in 0s (158 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_53gl7x8/libboost1.90-dev_1.90.0-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-2 [62.8 kB] Fetched 62.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmp2gp3yx/libibverbs1_63.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261.1-3 [3327 kB] Fetched 3327 kB in 0s (126 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp205hwswf/systemd_261.1-3_amd64.deb' Downloading dependency 132 of 265: libamd-comgr3:amd64=7.0.2+dfsg-3 Downloading dependency 133 of 265: libcc1-0:amd64=16.1.0-2 Downloading dependency 134 of 265: dwz:amd64=0.17-1 Downloading dependency 135 of 265: libuv1t64:amd64=1.52.1-4 Downloading dependency 136 of 265: libacl1:amd64=2.4.0-1 Downloading dependency 137 of 265: libprrte-dev:amd64=3.0.13-3 Downloading dependency 138 of 265: libkrb5-3:amd64=1.22.1-3 Downloading dependency 139 of 265: libctf-nobfd0:amd64=2.46.50.20260617-1 Downloading dependency 140 of 265: libldap2:amd64=2.6.13+dfsg-1 Downloading dependency 141 of 265: libprrte-bin:amd64=3.0.13-3 Downloading dependency 142 of 265: libtool:amd64=2.5.4-11 Downloading dependency 143 of 265: libncursesw6:amd64=6.6+20260608-2 Downloading dependency 144 of 265: g++:amd64=4:15.2.0-5+b1 Downloading dependency 145 of 265: libpam-runtime:amd64=1.7.0-8 Downloading dependency 146 of 265: libsimde-dev:amd64=0.8.4~rc3-5 Downloading dependency 147 of 265: libunistring5:amd64=1.4.2-1 Downloading dependency 148 of 265: procps:amd64=2:4.0.6-2 Downloading dependency 149 of 265: libxdmcp6:amd64=1:1.1.5-2+b1 Downloading dependency 150 of 265: gfortran-15-x86-64-linux-gnu:amd64=15.3.0-1 Downloading dependency 151 of 265: time:amd64=1.10-0.1 Downloading dependency 152 of 265: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 153 of 265: libltdl7:amd64=2.5.4-11 Downloading dependency 154 of 265: libcrypt1:amd64=1:4.5.1-1+b1 Downloading dependency 155 of 265: libngtcp2-16:amd64=1.22.1-1 Downloading dependency 156 of 265: libhwasan0:amd64=16.1.0-2 Downloading dependency 157 of 265: libgomp1:amd64=16.1.0-2 Downloading dependency 158 of 265: debhelper:amd64=14.3 Downloading dependency 159 of 265: libc-dev-bin:amd64=2.42-17 Downloading dependency 160 of 265: libdebconfclient0:amd64=0.283 Downloading dependency 161 of 265: libmpfr6:amd64=4.2.2-3 Downloading dependency 162 of 265: libncl2:amd64=2.1.21+git20210811.b1213a7-6+b2 Downloading dependency 163 of 265: libevent-dev:amd64=2.1.13-stable-1 Downloading dependency 164 of 265: dpkg-dev:amd64=1.23.7 Downloading dependency 165 of 265: libmunge2:amd64=0.5.18-1 Downloading dependency 166 of 265: g++-15-x86-64-linux-gnu:amd64=15.3.0-1 Downloading dependency 167 of 265: libpam0g:amd64=1.7.0-8 Downloading dependency 168 of 265: libproc2-1:amd64=2:4.0.6-2 Downloading dependency 169 of 265: libnettle8t64:amd64=3.10.2-1+b1 Downloading dependency 170 of 265: gcc-15-base:amd64=15.3.0-1 Downloading dependency 171 of 265: sensible-utils:amd64=0.0.26 Downloading dependency 172 of 265: findutils:amd64=4.10.0-4 Downloading dependency 173 of 265: cpp:amd64=4:15.2.0-5+b1 Downloading dependency 174 of 265: pci.ids:amd64=0.0~2026.07.06-1 Downloading dependency 175 of 265: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 176 of 265: rpcsvc-proto:amd64=1.4.4-1 Downloading dependency 177 of 265: libevent-openssl-2.1-7t64:amd64=2.1.13-stable-1 Downloading dependency 178 of 265: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 179 of 265: libclang-common-21-dev:amd64=1:21.1.8-7+b4 Downloading dependency 180 of 265: libpam-modules:amd64=1.7.0-8 Downloading dependency 181 of 265: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 182 of 265: liblzma5:amd64=5.8.3-1 Downloading dependency 183 of 265: libudev1:amd64=261.1-3 Downloading dependency 184 of 265: autopoint:amd64=1.0-3 Downloading dependency 185 of 265: libxau6:amd64=1:1.0.11-1+b2 Downloading dependency 186 of 265: cpp-15:amd64=15.3.0-1 Downloading dependency 187 of 265: base-files:amd64=14.2 Downloading dependency 188 of 265: xz-utils:amd64=5.8.3-1 Downloading dependency 189 of 265: libze1:amd64=1.28.2-2 Downloading dependency 190 of 265: libgcc-s1:amd64=16.1.0-2 Downloading dependency 191 of 265: liblsan0:amd64=16.1.0-2 Downloading dependency 192 of 265: libseccomp2:amd64=2.6.1-1 Downloading dependency 193 of 265: gcc-15:amd64=15.3.0-1 Downloading dependency 194 of 265: perl:amd64=5.40.1-8 Downloading dependency 195 of 265: dpkg:amd64=1.23.7 Downloading dependency 196 of 265: libtinfo6:amd64=6.6+20260608-2 Downloading dependency 197 of 265: libstdc++6:amd64=16.1.0-2 Downloading dependency 198 of 265: make:amd64=4.4.1-3 Downloading dependency 199 of 265: libxnvctrl0:amd64=535.171.04-1+b3 Downloading dependency 200 of 265: sysvinit-utils:amd64=3.18-1 Downloading dependency 201 of 265: libfabric1:amd64=2.1.0-1.1+b2 Downloading dependency 202 of 265: autotools-dev:amd64=20240727.1+nmu1 Downloading dependency 203 of 265: libattr1:amd64=1:2.6.0-1 Downloading dependency 204 of 265: libfido2-1:amd64=1.17.0-1 Downloading dependency 205 of 265: libzstd1:amd64=1.5.7+dfsg-3+b2 Downloading dependency 206 of 265: ibverbs-providers:amd64=63.0-2 Downloading dependency 207 of 265: g++-15:amd64=15.3.0-1 Downloading dependency 208 of 265: libgfortran-15-dev:amd64=15.3.0-1 Downloading dependency 209 of 265: libgprofng0:amd64=2.46.50.20260617-1 Downloading dependency 210 of 265: libmd0:amd64=1.2.0-2 Downloading dependency 211 of 265: g++-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 212 of 265: libevent-core-2.1-7t64:amd64=2.1.13-stable-1 Downloading dependency 213 of 265: libevent-extra-2.1-7t64:amd64=2.1.13-stable-1 Downloading dependency 214 of 265: libhwloc-plugins:amd64=2.14.0-2 Downloading dependency 215 of 265: base-passwd:amd64=3.6.8 Downloading dependency 216 of 265: libbinutils:amd64=2.46.50.20260617-1 Downloading dependency 217 of 265: libnl-3-200:amd64=3.12.0-2+b1 Downloading dependency 218 of 265: libnl-route-3-200:amd64=3.12.0-2+b1 Downloading dependency 219 of 265: libnuma-dev:amd64=2.0.19-1+b2 Downloading dependency 220 of 265: libpsl5t64:amd64=0.23.0-1 Downloading dependency 221 of 265: librdmacm1t64:amd64=63.0-2 Downloading dependency 222 of 265: libnuma1:amd64=2.0.19-1+b2 Downloading dependency 223 of 265: libcbor0.10:amd64=0.10.2-2.1+b1 Downloading dependency 224 of 265: libhwloc-dev:amd64=2.14.0-2 Downloading dependency 225 of 265: zlib1g:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 226 of 265: libbrotli1:amd64=1.2.0-3 Downloading dependency 227 of 265: init-system-helpers:amd64=1.69 Downloading dependency 228 of 265: libelf1t64:amd64=0.195-1 Downloading dependency 229 of 265: libffi8:amd64=3.7.1-2 Downloading dependency 230 of 265: libibverbs-dev:amd64=63.0-2 Downloading dependency 231 of 265: libpam-modules-bin:amd64=1.7.0-8 Downloading dependency 232 of 265: libucc1:amd64=1.8.0-2 Downloading dependency 233 of 265: libc6:amd64=2.42-17 Downloading dependency 234 of 265: liblz4-1:amd64=1.10.0-10 Downloading dependency 235 of 265: libuchardet0:amd64=0.0.8-2+b2 Downloading dependency 236 of 265: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 237 of 265: libgmp10:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 238 of 265: ncurses-bin:amd64=6.6+20260608-2 Downloading dependency 239 of 265: openssh-common:amd64=1:10.4p1-1 Downloading dependency 240 of 265: openssl-provider-legacy:amd64=3.6.3-1 Downloading dependency 241 of 265: tar:amd64=1.35+dfsg-4 Downloading dependency 242 of 265: libjsoncpp26:amd64=1.9.8-2 Downloading dependency 243 of 265: libngtcp2-crypto-ossl0:amd64=1.22.1-1 Downloading dependency 244 of 265: libuuid1:amd64=2.42.2-2 Downloading dependency 245 of 265: libgdbm-compat4t64:amd64=1.26-1+b2 Downloading dependency 246 of 265: cpp-15-x86-64-linux-gnu:amd64=15.3.0-1 Downloading dependency 247 of 265: libbz2-1.0:amd64=1.0.8-6+b2 Downloading dependency 248 of 265: libmpc3:amd64=1.3.1-3 Downloading dependency 249 of 265: debconf:amd64=1.5.92 Downloading dependency 250 of 265: libmount1:amd64=2.42.2-2 Downloading dependency 251 of 265: libcap-ng0:amd64=0.9.3-1+b1 Downloading dependency 252 of 265: libsasl2-modules-db:amd64=2.1.28+dfsg1-11 Downloading dependency 253 of 265: groff-base:amd64=1.24.1-1 Downloading dependency 254 of 265: libgmp-dev:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 255 of 265: libibumad3:amd64=63.0-2 Downloading dependency 256 of 265: libdrm-amdgpu1:amd64=2.4.134-3 Downloading dependency 257 of 265: libboost1.90-dev:amd64=1.90.0-6 Downloading dependency 258 of 265: libibverbs1:amd64=63.0-2 Downloading dependency 259 of 265: systemd:amd64=261.1-3 Downloading dependency 260 of 265: libitm1:amd64=16.1.0-2Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libitm1 amd64 16.1.0-2 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0roppu20/libitm1_16.1.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Fetched 709 kB in 0s (46.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjed32o2e/libdb5.3t64_5.3.28+dfsg2-11+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 gfortran-15 amd64 15.3.0-1 [22.2 kB] Fetched 22.2 kB in 0s (924 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpia3038vt/gfortran-15_15.3.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b4 [28.2 MB] Fetched 28.2 MB in 0s (169 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpsgd6u__j/libllvm21_21.1.8-7+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260712T202631Z unstable/main amd64 libquadmath0 amd64 16.1.0-2 [148 kB] Fetched 148 kB in 0s (14.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsrchsxge/libquadmath0_16.1.0-2_amd64.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 (600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp80akw792/dh-strip-nondeterminism_1.15.1-1_all.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/tmpyfm0tbka/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.gyLRbg32Uv as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.gyLRbg32Uv 127.0.0.1 - - [21/Jul/2026 10:39:42] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46443 ./ InRelease 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:46443 ./ Release [462 B] 127.0.0.1 - - [21/Jul/2026 10:39:42] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46443 ./ Release.gpg 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:46443 ./ Packages [326 kB] Fetched 327 kB in 0s (19.1 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 - 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127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./libsmartcols1_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./libudev1_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./libuuid1_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./util-linux_2.42.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./libdebconfclient0_0.283_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./libc-bin_2.42-17_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "GET /./ncurses-base_6.6%2b20260608-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:39:42] "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.gyLRbg32Uv 127.0.0.1 - - [21/Jul/2026 10:39:44] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 10:39:44] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46443 ./ InRelease 127.0.0.1 - - [21/Jul/2026 10:39:44] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:46443 ./ Release 127.0.0.1 - - [21/Jul/2026 10:39:44] code 404, message File not found 127.0.0.1 - - [21/Jul/2026 10:39:44] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46443 ./ 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.gyLRbg32Uv usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./libsystemd-shared_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./systemd_261.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./libexpat1_2.8.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./liblocale-gettext-perl_1.07-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./libstdc%2b%2b6_16.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./libuchardet0_0.0.8-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:05] "GET /./groff-base_1.24.1-1_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libpmix2t64_6.0.0%2breally5.0.9-3%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./googletest_1.17.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libgfortran5_16.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libgfortran-15-dev_15.3.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./gfortran-15-x86-64-linux-gnu_15.3.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./gfortran-15_15.3.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libibverbs1_63.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./ibverbs-providers_63.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./librdmacm1t64_63.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libfabric1_2.1.0-1.1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libucc1_1.8.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libibverbs-dev_63.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libprrte3_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libprrte-dev_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libnuma-dev_2.0.19-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libltdl7_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libltdl-dev_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libhwloc-dev_2.14.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libevent-2.1-7t64_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libevent-extra-2.1-7t64_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libevent-openssl-2.1-7t64_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libevent-dev_2.1.13-stable-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libprrte-bin_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libpkgconf7_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./pkgconf-bin_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./pkgconf_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libyaml-cpp0.9_0.9.0%2bdfsg-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libyaml-cpp-dev_0.9.0%2bdfsg-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./time_1.10-0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./libeigen3-dev_3.4.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [21/Jul/2026 10:40:07] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpyfm0tbka/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.gyLRbg32Uv Reading package lists... Building dependency tree... Reading state information... perl-base is already the newest version (5.40.1-8). libbsd0 is already the newest version (0.12.2-3). libbsd0 set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. gcc is already the newest version (4:15.2.0-5+b1). gcc 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. libblkid1 is already the newest version (2.42.2-2). libkrb5support0 is already the newest version (1.22.1-3). libkrb5support0 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. libsmartcols1 is already the newest version (2.42.2-2). libz3-4 is already the newest version (4.13.3-1.1). libz3-4 set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5+b1). gcc-x86-64-linux-gnu set to manually installed. libsystemd0 is already the newest version (261.1-3). libevent-pthreads-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-pthreads-2.1-7t64 set to manually installed. libncl-dev is already the newest version (2.1.21+git20210811.b1213a7-6+b2). libncl-dev set to manually installed. debianutils is already the newest version (5.23.2). libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libubsan1 is already the newest version (16.1.0-2). libubsan1 set to manually installed. libctf0 is already the newest version (2.46.50.20260617-1). libctf0 set to manually installed. libmagic1t64 is already the newest version (1:5.47-4). libmagic1t64 set to manually installed. binutils is already the newest version (2.46.50.20260617-1). binutils set to manually installed. libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. libucx0 is already the newest version (1.22.0~rc1-1). libucx0 set to manually installed. gettext is already the newest version (1.0-3). gettext set to manually installed. libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b2). libpmix2t64 set to manually installed. chrpath is already the newest version (0.18-1). chrpath set to manually installed. libasan8 is already the newest version (16.1.0-2). libasan8 set to manually installed. libhwloc15 is already the newest version (2.14.0-2). libhwloc15 set to manually installed. bsdextrautils is already the newest version (2.42.2-2). bsdextrautils set to manually installed. googletest is already the newest version (1.17.0-1). googletest set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. openssh-client is already the newest version (1:10.4p1-1). openssh-client set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. libdebhelper-perl is already the newest version (14.3). libdebhelper-perl set to manually installed. libdrm2 is already the newest version (2.4.134-3). libdrm2 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-10). liblocale-gettext-perl set to manually installed. libselinux1 is already the newest version (3.11-2). pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. cmake is already the newest version (4.3.4-1). cmake set to manually installed. libatomic1 is already the newest version (16.1.0-2). libatomic1 set to manually installed. libpciaccess0 is already the newest version (0.19-2). libpciaccess0 set to manually installed. gcc-16-base is already the newest version (16.1.0-2). libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46.50.20260617-1). binutils-x86-64-linux-gnu set to manually installed. librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. sed is already the newest version (4.9-3). libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.3.0-1). gcc-15-x86-64-linux-gnu set to manually installed. libjansson4 is already the newest version (2.15.1-1). libjansson4 set to manually installed. libxml2-16 is already the newest version (2.15.3+dfsg-1). libxml2-16 set to manually installed. libyaml-cpp-dev is already the newest version (0.9.0+dfsg-5). libyaml-cpp-dev set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. bash is already the newest version (5.3-3). libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. dash is already the newest version (0.5.12-12). libevent-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-2.1-7t64 set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. binutils-common is already the newest version (2.46.50.20260617-1). binutils-common set to manually installed. libyaml-cpp0.9 is already the newest version (0.9.0+dfsg-5). libyaml-cpp0.9 set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. coreutils is already the newest version (9.10-1). libgssapi-krb5-2 is already the newest version (1.22.1-3). libgssapi-krb5-2 set to manually installed. libmagic-mgc is already the newest version (1:5.47-4). libmagic-mgc set to manually installed. libc-bin is already the newest version (2.42-17). file is already the newest version (1:5.47-4). file set to manually installed. libarchive13t64 is already the newest version (3.8.8-2). libarchive13t64 set to manually installed. libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. libperl5.40 is already the newest version (5.40.1-8). libperl5.40 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-17). libibmad5 is already the newest version (63.0-2). libibmad5 set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. libedit2 is already the newest version (3.1-20260512-1). libedit2 set to manually installed. libcurl4t64 is already the newest version (8.21.0-2). libcurl4t64 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.2-3). zlib1g-dev set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b2). libgmpxx4ldbl set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. hostname is already the newest version (3.25). libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. libgfortran5 is already the newest version (16.1.0-2). libgfortran5 set to manually installed. libssl3t64 is already the newest version (3.6.3-1). mawk is already the newest version (1.3.4.20260302-1). libsframe3 is already the newest version (2.46.50.20260617-1). libsframe3 set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. linux-libc-dev is already the newest version (7.1.3-1). linux-libc-dev set to manually installed. autoconf is already the newest version (2.73-2). autoconf set to manually installed. util-linux is already the newest version (2.42.2-2). libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libsystemd-shared is already the newest version (261.1-3). libsystemd-shared set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b2). automake is already the newest version (1:1.18.1-4). automake set to manually installed. libdrm-common is already the newest version (2.4.134-3). libdrm-common set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libfile-stripnondeterminism-perl is already the newest version (1.15.1-1). libfile-stripnondeterminism-perl set to manually installed. libssh2-1t64 is already the newest version (1.11.1-4). libssh2-1t64 set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). ncurses-base is already the newest version (6.6+20260608-2). libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. diffutils is already the newest version (1:3.12-1). gettext-base is already the newest version (1.0-3). gettext-base set to manually installed. libgcc-15-dev is already the newest version (15.3.0-1). libgcc-15-dev set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. libstdc++-15-dev is already the newest version (15.3.0-1). libstdc++-15-dev set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. grep is already the newest version (3.12-1). help2man is already the newest version (1.49.3). help2man set to manually installed. libexpat1 is already the newest version (2.8.2-1). libexpat1 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libc6-dev is already the newest version (2.42-17). libc6-dev 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. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libk5crypto3 is already the newest version (1.22.1-3). libk5crypto3 set to manually installed. libtsan2 is already the newest version (16.1.0-2). libtsan2 set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. libcc1-0 is already the newest version (16.1.0-2). libcc1-0 set to manually installed. dwz is already the newest version (0.17-1). dwz set to manually installed. libuv1t64 is already the newest version (1.52.1-4). libuv1t64 set to manually installed. libacl1 is already the newest version (2.4.0-1). libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. libkrb5-3 is already the newest version (1.22.1-3). libkrb5-3 set to manually installed. libctf-nobfd0 is already the newest version (2.46.50.20260617-1). libctf-nobfd0 set to manually installed. libldap2 is already the newest version (2.6.13+dfsg-1). libldap2 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. libncursesw6 is already the newest version (6.6+20260608-2). libncursesw6 set to manually installed. g++ is already the newest version (4:15.2.0-5+b1). g++ set to manually installed. libpam-runtime is already the newest version (1.7.0-8). libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. procps is already the newest version (2:4.0.6-2). procps set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. gfortran-15-x86-64-linux-gnu is already the newest version (15.3.0-1). gfortran-15-x86-64-linux-gnu set to manually installed. time is already the newest version (1.10-0.1). time set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. libhwasan0 is already the newest version (16.1.0-2). libhwasan0 set to manually installed. libgomp1 is already the newest version (16.1.0-2). libgomp1 set to manually installed. debhelper is already the newest version (14.3). debhelper set to manually installed. libc-dev-bin is already the newest version (2.42-17). libc-dev-bin set to manually installed. libdebconfclient0 is already the newest version (0.283). libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. libncl2 is already the newest version (2.1.21+git20210811.b1213a7-6+b2). libncl2 set to manually installed. libevent-dev is already the newest version (2.1.13-stable-1). libevent-dev set to manually installed. dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.3.0-1). g++-15-x86-64-linux-gnu set to manually installed. libpam0g is already the newest version (1.7.0-8). libproc2-1 is already the newest version (2:4.0.6-2). libproc2-1 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. gcc-15-base is already the newest version (15.3.0-1). gcc-15-base set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. findutils is already the newest version (4.10.0-4). cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. pci.ids is already the newest version (0.0~2026.07.06-1). pci.ids 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. rpcsvc-proto is already the newest version (1.4.4-1). rpcsvc-proto set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-openssl-2.1-7t64 set to manually installed. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7+b4). libclang-common-21-dev set to manually installed. libpam-modules is already the newest version (1.7.0-8). libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. liblzma5 is already the newest version (5.8.3-1). libudev1 is already the newest version (261.1-3). autopoint is already the newest version (1.0-3). autopoint set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. cpp-15 is already the newest version (15.3.0-1). cpp-15 set to manually installed. base-files is already the newest version (14.2). xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. libgcc-s1 is already the newest version (16.1.0-2). liblsan0 is already the newest version (16.1.0-2). liblsan0 set to manually installed. libseccomp2 is already the newest version (2.6.1-1). libseccomp2 set to manually installed. gcc-15 is already the newest version (15.3.0-1). gcc-15 set to manually installed. perl is already the newest version (5.40.1-8). perl set to manually installed. dpkg is already the newest version (1.23.7). libtinfo6 is already the newest version (6.6+20260608-2). libstdc++6 is already the newest version (16.1.0-2). libstdc++6 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. sysvinit-utils is already the newest version (3.18-1). libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. libattr1 is already the newest version (1:2.6.0-1). libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b2). ibverbs-providers is already the newest version (63.0-2). ibverbs-providers set to manually installed. g++-15 is already the newest version (15.3.0-1). g++-15 set to manually installed. libgfortran-15-dev is already the newest version (15.3.0-1). libgfortran-15-dev set to manually installed. libgprofng0 is already the newest version (2.46.50.20260617-1). libgprofng0 set to manually installed. libmd0 is already the newest version (1.2.0-2). 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. libevent-core-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-core-2.1-7t64 set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.13-stable-1). libevent-extra-2.1-7t64 set to manually installed. libhwloc-plugins is already the newest version (2.14.0-2). libhwloc-plugins set to manually installed. base-passwd is already the newest version (3.6.8). libbinutils is already the newest version (2.46.50.20260617-1). libbinutils set to manually installed. libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 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. libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. libpsl5t64 is already the newest version (0.23.0-1). libpsl5t64 set to manually installed. librdmacm1t64 is already the newest version (63.0-2). librdmacm1t64 set to manually installed. libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. libhwloc-dev is already the newest version (2.14.0-2). libhwloc-dev set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. init-system-helpers is already the newest version (1.69). libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. libffi8 is already the newest version (3.7.1-2). libffi8 set to manually installed. libibverbs-dev is already the newest version (63.0-2). libibverbs-dev set to manually installed. libpam-modules-bin is already the newest version (1.7.0-8). libucc1 is already the newest version (1.8.0-2). libucc1 set to manually installed. libc6 is already the newest version (2.42-17). liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 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. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b2). ncurses-bin is already the newest version (6.6+20260608-2). openssh-common is already the newest version (1:10.4p1-1). openssh-common set to manually installed. openssl-provider-legacy is already the newest version (3.6.3-1). tar is already the newest version (1.35+dfsg-4). libjsoncpp26 is already the newest version (1.9.8-2). libjsoncpp26 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.22.1-1). libngtcp2-crypto-ossl0 set to manually installed. libuuid1 is already the newest version (2.42.2-2). libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.3.0-1). cpp-15-x86-64-linux-gnu set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b2). libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. debconf is already the newest version (1.5.92). libmount1 is already the newest version (2.42.2-2). libcap-ng0 is already the newest version (0.9.3-1+b1). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b2). libgmp-dev set to manually installed. libibumad3 is already the newest version (63.0-2). libibumad3 set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.134-3). libdrm-amdgpu1 set to manually installed. libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libibverbs1 is already the newest version (63.0-2). libibverbs1 set to manually installed. systemd is already the newest version (261.1-3). systemd set to manually installed. libitm1 is already the newest version (16.1.0-2). libitm1 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). gfortran-15 is already the newest version (15.3.0-1). gfortran-15 set to manually installed. libllvm21 is already the newest version (1:21.1.8-7+b4). libllvm21 set to manually installed. libquadmath0 is already the newest version (16.1.0-2). libquadmath0 set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.1-1). dh-strip-nondeterminism set to manually installed. The following NEW packages will be installed: pkg-config 127.0.0.1 - - [21/Jul/2026 10:41:14] "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:46443 ./ pkg-config 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (1779 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.gyLRbg32Uv/ 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 ... 41328 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.gyLRbg32Uv/ 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.gyLRbg32Uv (Reading database ... 41333 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.gyLRbg32Uv I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.gyLRbg32Uv 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.gyLRbg32Uv... I: success in 98.7535 seconds Downloading dependency 261 of 265: libdb5.3t64:amd64=5.3.28+dfsg2-11+b1 Downloading dependency 262 of 265: gfortran-15:amd64=15.3.0-1 Downloading dependency 263 of 265: libllvm21:amd64=1:21.1.8-7+b4 Downloading dependency 264 of 265: libquadmath0:amd64=16.1.0-2 Downloading dependency 265 of 265: dh-strip-nondeterminism:amd64=1.15.1-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdKT9Ddd/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1784059863 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuild8BRXKN/debrebuild.sbuildrc.rqmK96EvVlRX sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --binNMU-changelog= iqtree3 (3.1.1+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 -- amd64 / i386 Build Daemon (x86-ubc-01) Tue, 14 Jul 2026 20:11:03 +0000 --chroot=/srv/rebuilderd/tmp/debrebuild8BRXKN/debrebuild.tar.XDbpxSAWs0H5 --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/rebuilderdKT9Ddd/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: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl42-amd64.novalocal +==============================================================================+ | iqtree3 3.1.1+dfsg-2+b1 (amd64) Tue, 21 Jul 2026 10:41:21 +0000 | +==============================================================================+ Package: iqtree3 Version: 3.1.1+dfsg-2+b1 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/debrebuild8BRXKN/debrebuild.tar.XDbpxSAWs0H5 to /srv/rebuilderd/tmp/tmp.sbuild.L0XmsynJpG... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Tue, 21 Jul 2026 10:41:27 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs/iqtree3_3.1.1+dfsg-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 21 Jul 2026 10:41:28 +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-QXIetr/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Tue, 21 Jul 2026 10:41:31 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64) +------------------------------------------------------------------------------+ | Build environment Tue, 21 Jul 2026 10:41:32 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.95+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.95-1 (2026-07-04) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-2 build-essential_12.12 bzip2_1.0.8-6+b2 chrpath_0.18-1 cmake_4.3.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.17-1 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gfortran-15_15.3.0-1 gfortran-15-x86-64-linux-gnu_15.3.0-1 googletest_1.17.0-1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_63.0-2 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.8-2 libasan8_16.1.0-2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-2 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-3 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-2 libclang-common-21-dev_1:21.1.8-7+b4 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl4t64_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-3 libdrm-common_2.4.134-3 libdrm2_2.4.134-3 libedit2_3.1-20260512-1 libeigen3-dev_3.4.0-5 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.13-stable-1 libevent-core-2.1-7t64_2.1.13-stable-1 libevent-dev_2.1.13-stable-1 libevent-extra-2.1-7t64_2.1.13-stable-1 libevent-openssl-2.1-7t64_2.1.13-stable-1 libevent-pthreads-2.1-7t64_2.1.13-stable-1 libexpat1_2.8.2-1 libfabric1_2.1.0-1.1+b2 libffi8_3.7.1-2 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.3.0-1 libgfortran5_16.1.0-2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgomp1_16.1.0-2 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-2 libhwloc-dev_2.14.0-2 libhwloc-plugins_2.14.0-2 libhwloc15_2.14.0-2 libibmad5_63.0-2 libibumad3_63.0-2 libibverbs-dev_63.0-2 libibverbs1_63.0-2 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp26_1.9.8-2 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 libldap2_2.6.13+dfsg-1 libllvm21_1:21.1.8-7+b4 liblocale-gettext-perl_1.07-10 liblsan0_16.1.0-2 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-2 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncl-dev_2.1.21+git20210811.b1213a7-6+b2 libncl2_2.1.21+git20210811.b1213a7-6+b2 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpciaccess0_0.19-2 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3+b2 libproc2-1_2:4.0.6-2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.23.0-1 libpsm2-2_11.2.185-2.1 libquadmath0_16.1.0-2 librdmacm1t64_63.0-2 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsframe3_2.46.50.20260617-1 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.2-2 libsprng2_2.0a-19 libsprng2-dev_2.0a-19 libssh2-1t64_1.11.1-4 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd-shared_261.1-3 libsystemd0_261.1-3 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libucc1_1.8.0-2 libuchardet0_0.0.8-2+b2 libucx0_1.22.0~rc1-1 libudev1_261.1-3 libunistring5_1.4.2-1 libuuid1_2.42.2-2 libuv1t64_1.52.1-4 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.3+dfsg-1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libyaml-cpp-dev_0.9.0+dfsg-5 libyaml-cpp0.9_0.9.0+dfsg-5 libz3-4_4.13.3-1.1 libze1_1.28.2-2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mpi-default-dev_1.20 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.4p1-1 openssh-common_1:10.4p1-1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 pci.ids_0.0~2026.07.06-1 perl_5.40.1-8 perl-base_5.40.1-8 perl-modules-5.40_5.40.1-8 pkg-config_2.5.1-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 procps_2:4.0.6-2 rpcsvc-proto_1.4.4-1 sed_4.9-3 sensible-utils_0.0.26 systemd_261.1-3 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 time_1.10-0.1 util-linux_2.42.2-2 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Tue, 21 Jul 2026 10:41:32 +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 uGktbh9eBw8/850TZc133ga58+lNC6kZMNKyw4CFkIE/ldqRTYKjFV8WIn+k/mI1 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/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 Hack binNMU version ------------------- Created changelog entry for binNMU version 3.1.1+dfsg-2+b1 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1784059863 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+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/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 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt: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: 15.3.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- 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 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt: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: 15.3.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- 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 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt: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: 15.3.0 Target binary : 64-bit -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- 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 -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/kernelsse.dir/DependInfo.cmake "--color=" kernelsse 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[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/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 -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' 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 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[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' 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[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' 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' 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 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' [ 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.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[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' [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.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/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 [ 2%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/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 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 3%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.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 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 [ 3%] 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 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 [ 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 [ 4%] 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/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 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/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 [ 5%] 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 [ 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 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 [ 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 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 [ 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 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%] 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)); | ^~~~~~~~~~~~~~~~~~ [ 9%] 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 [ 9%] 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 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/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 [ 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 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 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); | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o [ 12%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.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 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); | ^~~~~~~~~~~~~~~ [ 13%] 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 [ 13%] 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/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); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.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/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 [ 14%] 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 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 [ 14%] 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 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); | ^~~~~~~~~~~~~~~ /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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.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/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 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/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 [ 17%] 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/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 [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.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/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.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/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 [ 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 [ 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 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 [ 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 [ 20%] 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 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 [ 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 [ 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 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 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 [ 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%] 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 [ 24%] 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 [ 24%] 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 [ 24%] 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' [ 24%] Built target ncl 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 [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o [ 25%] 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/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 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' [ 25%] Built target nclextra 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 [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o 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' 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 [ 25%] 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 [ 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 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 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 [ 27%] 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 [ 28%] 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 [ 28%] 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 [ 28%] 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%] Building C object whtest/CMakeFiles/whtest.dir/whtest.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.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 [ 29%] 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 [ 29%] 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] 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 [ 30%] 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 [ 31%] 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' [ 31%] Built target whtest [ 31%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.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/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 [ 31%] 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 /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' [ 31%] Built target lsd2 [ 31%] 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 [ 32%] 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 [ 32%] 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 [ 32%] 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 [ 33%] 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 [ 33%] 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.omp' [ 33%] Built target kernelfma [ 33%] 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 [ 33%] 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 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' [ 33%] 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 [ 33%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 33%] Built target kernelsse [ 34%] 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 [ 34%] 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 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 /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' [ 34%] 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' [ 34%] 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 [ 34%] 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 [ 35%] 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 [ 36%] 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 [ 36%] 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 [ 36%] 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 [ 36%] 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 [ 37%] 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 [ 37%] 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 [ 38%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc 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' [ 38%] 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' [ 40%] 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 /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' [ 40%] Built target kernelavx [ 40%] 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 /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; | ^~~~~~~~ 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' [ 41%] 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 [ 41%] 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 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); | ^~~~~~~~~~~~~~~ [ 41%] 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 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' [ 41%] 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 make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend [ 42%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o 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 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[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' [ 42%] 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 [ 43%] 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 [ 43%] 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' [ 43%] Built target pllavx 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 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' [ 43%] 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 [ 43%] 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 [ 43%] 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' [ 43%] Built target cmaple_utils [ 44%] 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 [ 45%] 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 /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' [ 45%] Built target pda [ 45%] 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 [ 45%] 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 [ 46%] 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 [ 46%] 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 [ 46%] 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 [ 47%] 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 [ 47%] 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 [ 47%] 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 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' [ 48%] 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 [ 48%] 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 [ 48%] 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 [ 49%] 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 [ 49%] 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 [ 49%] 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 [ 50%] 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 [ 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 [ 50%] 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 [ 51%] 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 [ 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 [ 51%] 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' [ 51%] Built target phyloYAML [ 52%] 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 [ 52%] 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 [ 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 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 [ 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 [ 53%] 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 [ 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 [ 54%] 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 [ 55%] 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 [ 55%] 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 /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' [ 55%] Built target decentTree 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' [ 55%] 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 [ 55%] 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 [ 56%] 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 [ 56%] 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 [ 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 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 [ 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 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 [ 58%] 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 [ 60%] 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 [ 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 [ 60%] 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 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) | ^~~~ 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) | ^~~~ 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) | ^~~~ 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' [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.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 [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.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_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 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_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 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) | ^~~~ [ 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/../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/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%] 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 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) | ^~~~ /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' [ 61%] 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' [ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 61%] 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 [ 62%] 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 [ 62%] 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 [ 62%] 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 [ 63%] 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' [ 63%] Built target cmaple_model [ 64%] 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 [ 64%] 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 [ 64%] 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 [ 65%] 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 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' [ 65%] 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 [ 65%] 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 [ 65%] 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 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) | ^~~~ [ 65%] 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 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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] 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 [ 66%] 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 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) | ^~~~ /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) | ~~^~~~~~~~~~~~ [ 67%] 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 [ 67%] 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 /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) | ~~^~~~~~~~~~~~ [ 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 [ 68%] 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 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) | ^~~~ [ 68%] 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 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) | ^~~~ [ 68%] 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 [ 69%] 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 [ 69%] 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 [ 69%] 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 [ 69%] 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 [ 70%] 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 "/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' [ 70%] 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.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' [ 70%] 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 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) | ^~~~ [ 71%] 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' [ 71%] 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.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 model/CMakeFiles/model.dir/rateheterotachy.cpp.o [ 72%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.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 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 [ 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 [ 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 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) | ^~~~ [ 73%] 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 [ 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/../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] 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’ 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 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 [ 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 [ 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 [ 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 /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' [ 76%] Built target cmaple [ 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 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-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 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/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 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 [ 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/pattern.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.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/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.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/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 [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.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/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.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/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.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 [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.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/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 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/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.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/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c 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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 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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 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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 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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.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/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/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/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 [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.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/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/phyloanalysis.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 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/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.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/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/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/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.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 [ 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/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/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/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) | ^~~~ [ 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[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 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/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 make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' 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' 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 -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]: 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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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]: 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 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 /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -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 [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.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/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 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 [ 2%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 3%] 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 -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]: 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 /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -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 make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 3%] 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 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.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 [ 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 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 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 [ 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/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 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.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 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/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 [ 6%] 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 [ 6%] 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 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.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 [ 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 [ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o /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' 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%] Built target booster [ 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 [ 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/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)); | ^~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ 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 C object pll/CMakeFiles/pll.dir/genericParallelization.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/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); | ^~~~~~~~~~~~~~~ [ 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 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); | ^~~~~~~~~~~~~~~ [ 11%] 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 [ 11%] 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); | ^~~~~~~~~~~~~~~ [ 11%] 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); | ^~~~~~~~~~~~~~~ [ 11%] 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 [ 12%] 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); | ^~~~~~~~~~~~~~~ [ 12%] 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); | ^~~~~~~~~~~~~~~ [ 12%] 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 [ 13%] 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 [ 13%] 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); | ^~~~~~~~~~~~~~~ [ 13%] 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 [ 14%] 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/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); | ^~~~~~~~~~~~~~~ [ 14%] 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/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); | ^~~~~~~~~~~~~~~ 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) * | ^~~~~~~~~~~~~~~~~~ [ 15%] 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 [ 15%] 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' [ 15%] Built target pll 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' [ 16%] 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 [ 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 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 [ 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 /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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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 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' [ 17%] 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 [ 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 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/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 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 [ 20%] 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 [ 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 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 [ 22%] 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 [ 22%] 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/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 [ 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%] 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' [ 23%] Built target nclextra [ 24%] 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 [ 24%] 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 [ 24%] 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 [ 24%] 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 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' [ 24%] 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 [ 24%] 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 [ 24%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 26%] 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' [ 26%] Built target sprng [ 27%] 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 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' [ 27%] 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 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 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 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 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' [ 27%] 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 [ 27%] 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 [ 28%] 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 [ 28%] 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 [ 28%] 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 [ 29%] 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 [ 29%] 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 [ 29%] 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 /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] 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 [ 29%] 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' [ 29%] Built target lsd2 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' [ 29%] 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 [ 30%] 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' [ 30%] 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.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' [ 30%] 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 [ 31%] 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 [ 31%] 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 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 [ 32%] 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 [ 32%] 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 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 [ 33%] 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 [ 34%] 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 [ 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/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 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 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' /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 whtest 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 [ 34%] Built target gsl 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 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 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 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 make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 36%] 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 /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 libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 36%] Built target kernelsse [ 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 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); | ^~~~~~~~~~~~~~~ [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.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 [ 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/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 [ 37%] 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 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' [ 37%] 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 [ 37%] 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' [ 37%] Built target pllavx 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 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' [ 37%] 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 [ 37%] 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' [ 37%] Built target cmaple_utils [ 38%] 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 [ 38%] 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 [ 40%] 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 [ 40%] 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 [ 41%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Built target kernelavx [ 41%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 43%] 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 [ 43%] 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' [ 43%] 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 [ 43%] Built target phyloYAML [ 43%] 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 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' [ 43%] 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 [ 43%] 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' [ 43%] Built target kernelfma [ 44%] 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 [ 45%] 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 [ 45%] 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 [ 45%] 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 [ 46%] 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 [ 46%] 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 [ 46%] 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 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' [ 47%] 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 [ 47%] 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 [ 47%] 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 [ 48%] 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 [ 48%] 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 [ 49%] 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 [ 49%] 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 [ 49%] 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 [ 49%] 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 [ 50%] 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' [ 50%] Built target pda [ 50%] 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 [ 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 [ 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 [ 51%] 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 [ 51%] 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 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' [ 51%] 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 [ 52%] 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 [ 52%] 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 [ 53%] 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 [ 53%] 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 [ 53%] 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 [ 54%] 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 [ 55%] 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' [ 55%] Built target decentTree [ 55%] 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 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) | ^~~~ [ 55%] 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 [ 56%] 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 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) | ^~~~ [ 56%] 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 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) | ^~~~ [ 56%] 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 [ 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 [ 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 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/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 [ 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 /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 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' [ 58%] 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 [ 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 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) | ^~~~ [ 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 [ 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 [ 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_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) | ^~~~ 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) | ^~~~ [ 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 [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.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/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%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.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/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 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 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/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/../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/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/../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 [ 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/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/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 [ 64%] 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/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 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/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 [ 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%] 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' [ 65%] Built target cmaple_tree [ 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 [ 66%] 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 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' [ 66%] 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 [ 66%] 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 [ 66%] 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 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.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' [ 67%] 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' [ 68%] 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 [ 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 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) | ^~~~ [ 69%] 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 [ 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 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] [ 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 [ 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 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’ [ 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 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 [ 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 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 [ 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 [ 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 /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' [ 75%] Built target cmaple [ 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 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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 -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.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 -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 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/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.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 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 [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.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/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/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 [ 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/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 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 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-ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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 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-Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.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 [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.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 [ 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 -DUSE_CMAPLE -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/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.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/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.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/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.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/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.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/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.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/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genometree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.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/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.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/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.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/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosuperhmm.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.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/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 [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.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/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeplen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.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/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.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/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 /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/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.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/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.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 /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/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 [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.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/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 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/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.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 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.serial' [ 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.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/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace 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/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.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' [ 94%] 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.serial/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.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 [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.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 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/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 [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.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/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.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 CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/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 [ 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/alisim.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/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.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 [ 96%] Building CXX object main/CMakeFiles/main.dir/timetree.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/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 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 [ 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/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 /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/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/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) | ^~~~ [ 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 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.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/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 -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[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/kernelavx.dir/DependInfo.cmake "--color=" kernelavx 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/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: 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/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster 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/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/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f CMakeFiles/kernelavx.dir/build.make 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'/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 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_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 CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/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 [ 2%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.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/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 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 /usr/bin/x86_64-linux-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 booster/CMakeFiles/booster.dir/bitset_index.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/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 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 [ 3%] 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 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)); | ^~~~~~~~~~~~~~~~~~ [ 3%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o [ 4%] Building C object booster/CMakeFiles/booster.dir/io.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 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 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.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 [ 5%] 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 [ 6%] 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 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 [ 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 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.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 [ 7%] 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 [ 8%] 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 /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 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 [ 8%] 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 [ 8%] 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)); | ^~~~~~~~~~~~~~~~~~ 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' [ 9%] 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 [ 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 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 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 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)); | ^~~~~~~~~~~~~~~~~~ [ 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 [ 11%] 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 [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.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/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); | ^~~~~~~~~~~~~~~ [ 12%] 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); | ^~~~~~~~~~~~~~~ [ 12%] 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 [ 12%] 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 /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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ [ 13%] 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 [ 13%] 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); | ^~~~~~~~~~~~~~~ [ 13%] 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); | ^~~~~~~~~~~~~~~ [ 14%] 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); | ^~~~~~~~~~~~~~~ [ 14%] 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); | ^~~~~~~~~~~~~~~ [ 15%] 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 [ 15%] 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 [ 16%] 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 [ 16%] 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); | ^~~~~~~~~~~~~~~ [ 16%] 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 [ 16%] 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); | ^~~~~~~~~~~~~~~ [ 17%] 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 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); | ^~~~~~~~~~~~~~~ [ 17%] 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) * | ^~~~~~~~~~~~~~~~~~ [ 17%] 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 [ 17%] 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' [ 17%] Built target pll [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o [ 18%] 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/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.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 [ 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 [ 20%] 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 [ 21%] 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 [ 21%] 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 [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.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/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 [ 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 [ 22%] 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 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 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' [ 22%] 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 [ 22%] 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 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 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 [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake 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 /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' [ 24%] Built target ncl 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' [ 24%] 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 [ 24%] 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 [ 24%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 26%] 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' [ 26%] 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.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' [ 26%] 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 [ 26%] 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' [ 26%] Built target lsd2 [ 26%] 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 [ 26%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 26%] Built target lbfgsb 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 -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' 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 [ 26%] 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 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 '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 26%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/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 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 [ 27%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/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.mpi' [ 27%] 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.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 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' 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.mpi' [ 27%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.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/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 [ 27%] 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 [ 28%] 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 /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.mpi' [ 28%] Built target nclextra [ 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 [ 29%] 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 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' [ 30%] 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 [ 31%] 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 [ 31%] 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 /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; | ^~~~~~~~ [ 31%] 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 [ 31%] 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 [ 31%] 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 /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 32%] 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 [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.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.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 [ 33%] 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' [ 33%] Built target gsl 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' [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o [ 34%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.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 CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c 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 /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ [ 34%] 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 [ 34%] 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 [ 34%] 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 [ 34%] 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' [ 34%] Built target pllavx [ 35%] 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 -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/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 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 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 35%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/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 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 [ 36%] 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 /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' [ 36%] Built target whtest 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 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-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 [ 36%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake 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-ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 [ 37%] 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 [ 37%] 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 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' [ 37%] Built target cmaple_utils 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' [ 37%] 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 [ 37%] 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 [ 38%] 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 -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 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' [ 40%] 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 [ 40%] 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 [ 41%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 [ 41%] Building CXX object utils/CMakeFiles/decentTree.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 -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 /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' [ 41%] Built target kernelavx 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' [ 41%] 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 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 42%] 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 [ 42%] 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 [ 42%] 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 -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 [ 42%] 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 /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' [ 42%] Built target phyloYAML [ 43%] 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 [ 43%] 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 [ 43%] 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.mpi' [ 43%] Built target kernelfma [ 43%] 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 [ 43%] 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 [ 43%] 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 [ 44%] 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 [ 44%] 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 [ 44%] 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 CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/greedy.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.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 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 [ 45%] 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 [ 45%] 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 [ 46%] 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 [ 47%] 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 [ 47%] 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 [ 48%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.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/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 [ 48%] 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 [ 48%] 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 [ 48%] 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 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) | ^~~~ [ 48%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.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/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 [ 48%] 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 [ 49%] 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' [ 49%] Built target decentTree [ 50%] 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 [ 51%] 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 [ 51%] 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 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) | ^~~~ [ 51%] 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 [ 51%] 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/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) | ^~~~ [ 52%] Building CXX object pda/CMakeFiles/pda.dir/pruning.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/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 [ 52%] 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 [ 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 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) | ^~~~ [ 54%] 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 [ 54%] 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 [ 54%] 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 "/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' [ 54%] 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' [ 54%] 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 [ 54%] 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/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) | ^~~~ [ 54%] 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 [ 54%] 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' [ 54%] Built target terraphast [ 54%] 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 [ 54%] 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 [ 54%] 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 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) | ^~~~ [ 55%] 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 [ 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 [ 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 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 [ 57%] 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 [ 57%] 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 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) | ^~~~ [ 57%] 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 [ 57%] 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 [ 58%] 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 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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] 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_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 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 [ 60%] 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 [ 61%] 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 "/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 [ 61%] 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 [ 61%] 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 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 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 [ 62%] 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 [ 62%] 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 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) | ^~~~ 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) | ^~~~ [ 63%] 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 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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /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' [ 63%] Built target pda /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 [ 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/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.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/modelbin.cpp.o [ 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/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 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 [ 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%] 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' [ 65%] 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.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 [ 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 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%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.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/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 [ 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 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' [ 68%] 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 [ 68%] 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 [ 68%] 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/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.mpi/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 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.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 [ 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 [ 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%] 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 [ 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 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’ 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 [ 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 [ 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 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/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 [ 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 /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' [ 74%] Built target cmaple [ 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 [ 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 [ 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 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.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' [ 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/alisimulatorheterogeneity.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 [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.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/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 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 [ 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 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 [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.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/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 [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 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/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.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 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-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.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/iqtree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.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/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/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 /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 [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o [ 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/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 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 -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/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genometree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.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/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 -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/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosuperhmm.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.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/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 [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.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/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeplen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.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/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.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/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.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/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.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/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.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 /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/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.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/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 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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/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 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-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.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 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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 -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/presenceabsencematrix.cpp.o [ 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 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 [ 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 [ 96%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.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/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.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/alisim.cpp.o [ 96%] 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/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 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 [ 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 /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/../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-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 Jul 14 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: 770468 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Jul 21 10:54:27 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 0.000447356 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 4.05961e-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 7.7995e-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: -11227.494 Optimal log-likelihood: -11227.413 Rate parameters: A-C: 1.40018 A-G: 2.24254 A-T: 1.69106 C-G: 1.83276 C-T: 2.70820 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: 1.529 Parameters optimization took 1 rounds (0.017 sec) Time for fast ML tree search: 0.182 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 11883.982 85 23937.965 23987.025 24273.769 2 JC+I 11630.580 86 23433.159 23483.543 23772.915 3 JC+G4 11316.056 86 22804.113 22854.496 23143.868 4 JC+I+G4 11300.019 87 22774.038 22825.768 23117.744 5 JC+R2 11408.988 87 22991.976 23043.706 23335.682 6 JC+R3 11310.484 89 22798.969 22853.459 23150.576 7 JC+R4 11296.310 91 22774.621 22831.963 23134.129 8 JC+R5 11295.876 93 22777.751 22838.041 23145.161 14 JC+I+R2 11341.105 88 22858.210 22911.309 23205.867 15 JC+I+R3 11299.058 90 22778.116 22834.020 23133.674 16 JC+I+R4 11295.101 92 22774.202 22833.007 23137.662 26 JC+I+G4 11300.019 87 22774.038 22825.768 23117.744 48 F81+I+G4 11300.020 87 22774.039 22825.769 23117.745 70 F81+F+I+G4 11296.201 90 22772.403 22828.307 23127.960 92 K2P+I+G4 11254.187 88 22684.374 22737.472 23032.030 114 K2P+I+G4 11254.187 88 22684.374 22737.472 23032.030 136 HKY+I+G4 11254.187 88 22684.373 22737.472 23032.030 158 HKY+F+I+G4 11247.660 91 22677.320 22734.663 23036.829 180 TNe+I+G4 11252.199 89 22682.398 22736.888 23034.005 202 TNe+I+G4 11252.199 89 22682.398 22736.888 23034.005 224 TN+I+G4 11252.198 89 22682.396 22736.886 23034.003 246 TN+F+I+G4 11244.888 92 22673.776 22732.580 23037.235 268 K3P+I+G4 11241.125 89 22660.250 22714.740 23011.857 290 K3P+I+G4 11241.125 89 22660.250 22714.740 23011.857 312 K3Pu+I+G4 11241.124 89 22660.249 22714.738 23011.856 334 K3Pu+F+I+G4 11235.341 92 22654.681 22713.486 23018.141 356 TPM2+I+G4 11254.066 89 22686.132 22740.622 23037.739 378 TPM2+I+G4 11254.066 89 22686.132 22740.622 23037.739 400 TPM2u+I+G4 11254.066 89 22686.131 22740.621 23037.739 422 TPM2u+F+I+G4 11247.415 92 22678.830 22737.634 23042.289 444 TPM3+I+G4 11247.127 89 22672.254 22726.743 23023.861 466 TPM3+I+G4 11247.127 89 22672.254 22726.743 23023.861 488 TPM3u+I+G4 11247.126 89 22672.251 22726.741 23023.858 510 TPM3u+F+I+G4 11244.245 92 22672.489 22731.294 23035.949 532 TIMe+I+G4 11239.225 90 22658.450 22714.354 23014.007 554 TIMe+I+G4 11239.225 90 22658.450 22714.354 23014.007 576 TIM+I+G4 11239.224 90 22658.448 22714.353 23014.006 598 TIM+F+I+G4 11232.679 93 22651.359 22711.649 23018.769 620 TIM2e+I+G4 11252.092 90 22684.183 22740.088 23039.741 642 TIM2e+I+G4 11252.092 90 22684.183 22740.088 23039.741 664 TIM2+I+G4 11252.090 90 22684.181 22740.085 23039.739 686 TIM2+F+I+G4 11244.666 93 22675.332 22735.621 23042.741 708 TIM3e+I+G4 11244.970 90 22669.940 22725.844 23025.498 730 TIM3e+I+G4 11244.970 90 22669.940 22725.844 23025.498 752 TIM3+I+G4 11244.968 90 22669.936 22725.841 23025.494 774 TIM3+F+I+G4 11241.397 93 22668.794 22729.083 23036.203 796 TVMe+I+G4 11232.381 91 22646.761 22704.104 23006.270 818 TVMe+I+G4 11232.381 91 22646.761 22704.104 23006.270 840 TVM+I+G4 11232.378 91 22646.757 22704.099 23006.265 862 TVM+F+I+G4 11230.053 94 22648.105 22709.905 23019.466 884 SYM+I+G4 11230.313 92 22644.625 22703.429 23008.084 906 SYM+I+G4 11230.313 92 22644.625 22703.429 23008.084 928 GTR+I+G4 11230.311 92 22644.622 22703.426 23008.081 950 GTR+F+I+G4 11227.348 95 22644.696 22708.029 23020.007 Akaike Information Criterion: GTR+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: 3.634 seconds (0h:0m:3s) Wall-clock time for ModelFinder: 3.667 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, 1.533 / Estimate: 0.000, 0.931 / LogL: -11245.234 Init pinv, alpha: 0.012, 1.533 / Estimate: 0.084, 1.520 / LogL: -11230.058 Init pinv, alpha: 0.023, 1.533 / Estimate: 0.085, 1.524 / LogL: -11230.053 Init pinv, alpha: 0.035, 1.533 / Estimate: 0.084, 1.522 / LogL: -11230.054 Init pinv, alpha: 0.046, 1.533 / Estimate: 0.085, 1.525 / LogL: -11230.053 Init pinv, alpha: 0.058, 1.533 / Estimate: 0.084, 1.523 / LogL: -11230.055 Init pinv, alpha: 0.069, 1.533 / Estimate: 0.084, 1.519 / LogL: -11230.059 Init pinv, alpha: 0.081, 1.533 / Estimate: 0.084, 1.522 / LogL: -11230.056 Init pinv, alpha: 0.093, 1.533 / Estimate: 0.085, 1.534 / LogL: -11230.051 Init pinv, alpha: 0.104, 1.533 / Estimate: 0.086, 1.539 / LogL: -11230.057 Optimal pinv,alpha: 0.085, 1.534 / LogL: -11230.051 Parameters optimization took 0.642 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00846282 secs using 99.85% CPU Computing ML distances took 0.008954 sec (of wall-clock time) 0.008588 sec (of CPU time) Setting up auxiliary I and S matrices: done in 7.76681e-05 secs using 99.14% CPU Constructing RapidNJ tree: done in 0.000195193 secs using 99.9% CPU Computing RapidNJ tree took 0.000526 sec (of wall-clock time) 0.001429 sec (of CPU time) Log-likelihood of RapidNJ tree: -11279.052 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.376 second Computing log-likelihood of 98 initial trees ... 0.442 seconds Current best score: -11230.051 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11228.988 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11222.400 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 3: -11219.096 Iteration 10 / LogL: -11230.462 / Time: 0h:0m:5s Iteration 20 / LogL: -11229.678 / Time: 0h:0m:6s Finish initializing candidate tree set (16) Current best tree score: -11219.096 / CPU time: 2.258 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11222.729 / Time: 0h:0m:7s (0h:0m:9s left) Iteration 40 / LogL: -11219.206 / Time: 0h:0m:8s (0h:0m:7s left) Iteration 50 / LogL: -11222.093 / Time: 0h:0m:9s (0h:0m:6s left) Iteration 60 / LogL: -11226.553 / Time: 0h:0m:10s (0h:0m:4s left) Iteration 70 / LogL: -11219.192 / Time: 0h:0m:10s (0h:0m:3s left) Iteration 80 / LogL: -11220.855 / Time: 0h:0m:11s (0h:0m:2s left) Iteration 90 / LogL: -11219.464 / Time: 0h:0m:12s (0h:0m:1s left) Iteration 100 / LogL: -11223.711 / Time: 0h:0m:13s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 104 ITERATIONS / Time: 0h:0m:14s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11219.096 Optimal log-likelihood: -11219.094 Rate parameters: A-C: 1.41994 A-G: 2.54367 A-T: 1.68466 C-G: 1.82579 C-T: 2.54367 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 (0.015 sec) BEST SCORE FOUND : -11219.094 Total tree length: 12.882 Total number of iterations: 104 CPU time used for tree search: 9.459 sec (0h:0m:9s) Wall-clock time used for tree search: 9.702 sec (0h:0m:9s) Total CPU time used: 13.792 sec (0h:0m:13s) Total wall-clock time used: 14.072 sec (0h:0m:14s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Tue Jul 21 10:54:41 2026 13.79user 0.25system 0:14.08elapsed 99%CPU (0avgtext+0avgdata 17848maxresident)k 0inputs+240outputs (0major+2521minor)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 Jul 14 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: 853860 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Jul 21 10:54:41 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 0.000470188 secs using 79.54% 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 4.33309e-05 secs using 96.93% 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 9.28689e-05 secs using 100.1% 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: -11221.857 Optimal log-likelihood: -11221.536 Rate parameters: A-C: 1.54228 A-G: 2.47184 A-T: 1.85999 C-G: 2.03335 C-T: 2.99249 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.086 Gamma shape alpha: 1.546 Parameters optimization took 1 rounds (0.027 sec) Time for fast ML tree search: 0.221 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 11881.303 85 23932.605 23981.666 24268.410 2 JC+I 11628.891 86 23429.781 23480.165 23769.537 3 JC+G4 11313.932 86 22799.864 22850.248 23139.619 4 JC+I+G4 11298.050 87 22770.100 22821.830 23113.806 5 JC+R2 11407.334 87 22988.667 23040.397 23332.373 6 JC+R3 11306.646 89 22791.292 22845.782 23142.899 7 JC+R4 11294.890 91 22771.781 22829.123 23131.289 8 JC+R5 11294.427 93 22774.854 22835.143 23142.263 14 JC+I+R2 11337.438 88 22850.876 22903.975 23198.533 15 JC+I+R3 11296.639 90 22773.278 22829.182 23128.835 16 JC+I+R4 11293.019 92 22770.038 22828.842 23133.497 26 JC+I+G4 11298.050 87 22770.100 22821.830 23113.806 48 F81+I+G4 11298.052 87 22770.104 22821.834 23113.810 70 F81+F+I+G4 11293.915 90 22767.830 22823.734 23123.388 92 K2P+I+G4 11250.598 88 22677.196 22730.295 23024.853 114 K2P+I+G4 11250.598 88 22677.196 22730.295 23024.853 136 HKY+I+G4 11250.598 88 22677.196 22730.294 23024.852 158 HKY+F+I+G4 11243.670 91 22669.341 22726.683 23028.849 180 TNe+I+G4 11248.524 89 22675.048 22729.538 23026.655 202 TNe+I+G4 11248.524 89 22675.048 22729.538 23026.655 224 TN+I+G4 11248.523 89 22675.046 22729.535 23026.653 246 TN+F+I+G4 11240.776 92 22665.551 22724.356 23029.011 268 K3P+I+G4 11236.677 89 22651.354 22705.844 23002.961 290 K3P+I+G4 11236.677 89 22651.354 22705.843 23002.961 312 K3Pu+I+G4 11236.676 89 22651.351 22705.841 23002.958 334 K3Pu+F+I+G4 11230.553 92 22645.106 22703.910 23008.565 356 TPM2+I+G4 11250.452 89 22678.904 22733.394 23030.512 378 TPM2+I+G4 11250.452 89 22678.904 22733.394 23030.512 400 TPM2u+I+G4 11250.452 89 22678.903 22733.393 23030.510 422 TPM2u+F+I+G4 11243.385 92 22670.770 22729.574 23034.229 444 TPM3+I+G4 11242.652 89 22663.303 22717.793 23014.910 466 TPM3+I+G4 11242.652 89 22663.303 22717.793 23014.910 488 TPM3u+I+G4 11242.650 89 22663.301 22717.790 23014.908 510 TPM3u+F+I+G4 11239.626 92 22663.253 22722.057 23026.712 532 TIMe+I+G4 11234.690 90 22649.381 22705.285 23004.939 554 TIMe+I+G4 11234.690 90 22649.381 22705.285 23004.939 576 TIM+I+G4 11234.689 90 22649.378 22705.282 23004.935 598 TIM+F+I+G4 11227.773 93 22641.546 22701.836 23008.956 620 TIM2e+I+G4 11248.389 90 22676.778 22732.683 23032.336 642 TIM2e+I+G4 11248.389 90 22676.778 22732.683 23032.336 664 TIM2+I+G4 11248.389 90 22676.777 22732.681 23032.335 686 TIM2+F+I+G4 11240.512 93 22667.024 22727.313 23034.434 708 TIM3e+I+G4 11240.392 90 22660.784 22716.688 23016.342 730 TIM3e+I+G4 11240.392 90 22660.784 22716.688 23016.342 752 TIM3+I+G4 11240.390 90 22660.781 22716.685 23016.338 774 TIM3+F+I+G4 11236.646 93 22659.292 22719.582 23026.702 796 TVMe+I+G4 11226.784 91 22635.567 22692.910 22995.076 818 TVMe+I+G4 11226.784 91 22635.567 22692.910 22995.076 840 TVM+I+G4 11226.781 91 22635.562 22692.904 22995.070 862 TVM+F+I+G4 11224.352 94 22636.704 22698.503 23008.064 884 SYM+I+G4 11224.608 92 22633.216 22692.021 22996.676 906 SYM+I+G4 11224.608 92 22633.216 22692.021 22996.676 928 GTR+I+G4 11224.606 92 22633.212 22692.017 22996.672 950 GTR+F+I+G4 11221.511 95 22633.023 22696.356 23008.334 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: 3.671 seconds (0h:0m:3s) Wall-clock time for ModelFinder: 3.702 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, 0.939 / LogL: -11239.329 Init pinv, alpha: 0.012, 1.537 / Estimate: 0.084, 1.530 / LogL: -11224.351 Init pinv, alpha: 0.023, 1.537 / Estimate: 0.084, 1.527 / LogL: -11224.353 Init pinv, alpha: 0.035, 1.537 / Estimate: 0.084, 1.525 / LogL: -11224.354 Init pinv, alpha: 0.046, 1.537 / Estimate: 0.084, 1.529 / LogL: -11224.352 Init pinv, alpha: 0.058, 1.537 / Estimate: 0.084, 1.526 / LogL: -11224.354 Init pinv, alpha: 0.069, 1.537 / Estimate: 0.084, 1.522 / LogL: -11224.359 Init pinv, alpha: 0.081, 1.537 / Estimate: 0.084, 1.526 / LogL: -11224.355 Init pinv, alpha: 0.093, 1.537 / Estimate: 0.085, 1.538 / LogL: -11224.351 Init pinv, alpha: 0.104, 1.537 / Estimate: 0.086, 1.544 / LogL: -11224.356 Optimal pinv,alpha: 0.085, 1.538 / LogL: -11224.351 Parameters optimization took 0.644 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00868993 secs using 99.58% CPU Computing ML distances took 0.008897 sec (of wall-clock time) 0.008793 sec (of CPU time) Setting up auxiliary I and S matrices: done in 9.46431e-05 secs using 99.32% CPU Constructing RapidNJ tree: done in 0.000206333 secs using 99.35% CPU Computing RapidNJ tree took 0.000479 sec (of wall-clock time) 0.000372 sec (of CPU time) Log-likelihood of RapidNJ tree: -11279.174 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.341 second Computing log-likelihood of 98 initial trees ... 0.433 seconds Current best score: -11224.351 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 3: -11222.536 Iteration 10 / LogL: -11229.989 / Time: 0h:0m:5s Iteration 20 / LogL: -11222.874 / Time: 0h:0m:6s Finish initializing candidate tree set (13) Current best tree score: -11222.536 / CPU time: 2.116 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 24: -11222.144 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 29: -11220.919 Iteration 30 / LogL: -11222.420 / Time: 0h:0m:7s (0h:0m:12s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 39: -11220.712 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 40: -11220.540 Iteration 40 / LogL: -11220.540 / Time: 0h:0m:8s (0h:0m:11s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 42: -11219.398 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 43: -11219.105 Iteration 50 / LogL: -11221.027 / Time: 0h:0m:9s (0h:0m:10s left) Iteration 60 / LogL: -11219.715 / Time: 0h:0m:10s (0h:0m:8s left) Iteration 70 / LogL: -11220.940 / Time: 0h:0m:10s (0h:0m:7s left) Iteration 80 / LogL: -11238.168 / Time: 0h:0m:11s (0h:0m:6s left) Iteration 90 / LogL: -11219.154 / Time: 0h:0m:12s (0h:0m:5s left) Iteration 100 / LogL: -11220.880 / Time: 0h:0m:13s (0h:0m:4s left) Iteration 110 / LogL: -11242.781 / Time: 0h:0m:14s (0h:0m:3s left) Iteration 120 / LogL: -11219.245 / Time: 0h:0m:15s (0h:0m:2s left) Iteration 130 / LogL: -11219.107 / Time: 0h:0m:16s (0h:0m:1s left) Iteration 140 / LogL: -11224.419 / Time: 0h:0m:16s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 144 ITERATIONS / Time: 0h:0m:17s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11219.105 Optimal log-likelihood: -11219.100 Rate parameters: A-C: 1.42912 A-G: 2.55207 A-T: 1.69377 C-G: 1.83662 C-T: 2.55207 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 (0.016 sec) BEST SCORE FOUND : -11219.100 Total tree length: 12.885 Total number of iterations: 144 CPU time used for tree search: 12.604 sec (0h:0m:12s) Wall-clock time used for tree search: 12.839 sec (0h:0m:12s) Total CPU time used: 16.961 sec (0h:0m:16s) Total wall-clock time used: 17.244 sec (0h:0m:17s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Tue Jul 21 10:54:59 2026 16.96user 0.25system 0:17.25elapsed 99%CPU (0avgtext+0avgdata 19804maxresident)k 0inputs+288outputs (0major+2608minor)pagefaults 0swaps + rm -rf /tmp/iqtree3-test.IbzHDA 30.79user 0.52system 0:31.37elapsed 99%CPU (0avgtext+0avgdata 19804maxresident)k 0inputs+576outputs (0major+6823minor)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-dbgsym' in '../iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'iqtree3' in '../iqtree3_3.1.1+dfsg-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree3_3.1.1+dfsg-2+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-07-21T10:56:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 21 Jul 2026 10:56:53 +0000 | +------------------------------------------------------------------------------+ iqtree3_3.1.1+dfsg-2+b1_amd64.changes: -------------------------------------- Format: 1.8 Date: Tue, 14 Jul 2026 20:11:03 +0000 Source: iqtree3 (3.1.1+dfsg-2) Binary: iqtree3 iqtree3-dbgsym Binary-Only: yes Architecture: amd64 Version: 3.1.1+dfsg-2+b1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: amd64 / i386 Build Daemon (x86-ubc-01) Description: iqtree3 - efficient phylogenetic software by maximum likelihood; v3 Changes: iqtree3 (3.1.1+dfsg-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 Checksums-Sha1: 4a8afaa9c95792bd884fcb1ab7c893101c20baed 122127244 iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb 7711f77983d15c6fe62be1464fd36c7df3c76562 8951 iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo a84400cc6de80480321e9f18d935d8a42e63101c 10723328 iqtree3_3.1.1+dfsg-2+b1_amd64.deb Checksums-Sha256: 25e24eac0aeb52edd193ca218df63a07300f380af91413963a10c72dbbd1eb09 122127244 iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb a65e73d3e8be3970d58ce95720d0e40298ede0949e4ff863416c377332beb950 8951 iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo 5b25b73dc2803856b69e7d52f1eba6cbdb97eee36c2497f21f9d7a4495820af9 10723328 iqtree3_3.1.1+dfsg-2+b1_amd64.deb Files: 1975c183d515f3b10d8a527a4f04cff7 122127244 debug optional iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb 863bdb4162fcec5be47a1a72a98e9be1 8951 science optional iqtree3_3.1.1+dfsg-2+b1_amd64.buildinfo 8eff9a5ff8c7dc23cf84d06f3bc1c223 10723328 science optional iqtree3_3.1.1+dfsg-2+b1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 21 Jul 2026 10:56:54 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree3 (3.1.1+dfsg-2) Binary: iqtree3 iqtree3-dbgsym Architecture: amd64 Version: 3.1.1+dfsg-2+b1 Binary-Only-Changes: iqtree3 (3.1.1+dfsg-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libyaml-cpp0.9 . -- amd64 / i386 Build Daemon (x86-ubc-01) Tue, 14 Jul 2026 20:11:03 +0000 Checksums-Md5: 1975c183d515f3b10d8a527a4f04cff7 122127244 iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb 8eff9a5ff8c7dc23cf84d06f3bc1c223 10723328 iqtree3_3.1.1+dfsg-2+b1_amd64.deb Checksums-Sha1: 4a8afaa9c95792bd884fcb1ab7c893101c20baed 122127244 iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb a84400cc6de80480321e9f18d935d8a42e63101c 10723328 iqtree3_3.1.1+dfsg-2+b1_amd64.deb Checksums-Sha256: 25e24eac0aeb52edd193ca218df63a07300f380af91413963a10c72dbbd1eb09 122127244 iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb 5b25b73dc2803856b69e7d52f1eba6cbdb97eee36c2497f21f9d7a4495820af9 10723328 iqtree3_3.1.1+dfsg-2+b1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 21 Jul 2026 10:56:51 +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 (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-2), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), chrpath (= 0.18-1), cmake (= 4.3.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), gfortran-15 (= 15.3.0-1), gfortran-15-x86-64-linux-gnu (= 15.3.0-1), googletest (= 1.17.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 63.0-2), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.8-2), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-2), libboost-dev (= 1.90.0.2), libboost1.90-dev (= 1.90.0-6), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-2), libclang-common-21-dev (= 1:21.1.8-7+b4), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl4t64 (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-3), libdrm-common (= 2.4.134-3), libdrm2 (= 2.4.134-3), libedit2 (= 3.1-20260512-1), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libevent-core-2.1-7t64 (= 2.1.13-stable-1), libevent-dev (= 2.1.13-stable-1), libevent-extra-2.1-7t64 (= 2.1.13-stable-1), libevent-openssl-2.1-7t64 (= 2.1.13-stable-1), libevent-pthreads-2.1-7t64 (= 2.1.13-stable-1), libexpat1 (= 2.8.2-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.7.1-2), libfido2-1 (= 1.17.0-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.2-2), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-15-dev (= 15.3.0-1), libgfortran5 (= 16.1.0-2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16.1.0-2), libhwloc-dev (= 2.14.0-2), libhwloc-plugins (= 2.14.0-2), libhwloc15 (= 2.14.0-2), libibmad5 (= 63.0-2), libibumad3 (= 63.0-2), libibverbs-dev (= 63.0-2), libibverbs1 (= 63.0-2), libidn2-0 (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp26 (= 1.9.8-2), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap2 (= 2.6.13+dfsg-1), libllvm21 (= 1:21.1.8-7+b4), liblocale-gettext-perl (= 1.07-10), liblsan0 (= 16.1.0-2), libltdl-dev (= 2.5.4-11), libltdl7 (= 2.5.4-11), liblz4-1 (= 1.10.0-10), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-2), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncl-dev (= 2.1.21+git20210811.b1213a7-6+b2), libncl2 (= 2.1.21+git20210811.b1213a7-6+b2), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-ossl0 (= 1.22.1-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpciaccess0 (= 0.19-2), libpcre2-8-0 (= 10.46-1+b2), libperl5.40 (= 5.40.1-8), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 6.0.0+really5.0.9-3+b2), libproc2-1 (= 2:4.0.6-2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.23.0-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16.1.0-2), librdmacm1t64 (= 63.0-2), librhash1 (= 1.4.6-1.1+b1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.2-2), libsprng2 (= 2.0a-19), libsprng2-dev (= 2.0a-19), libssh2-1t64 (= 1.11.1-4), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd-shared (= 261.1-3), libsystemd0 (= 261.1-3), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libucc1 (= 1.8.0-2), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.22.0~rc1-1), libudev1 (= 261.1-3), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-2), libuv1t64 (= 1.52.1-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libxxhash0 (= 0.8.3-2+b2), libyaml-cpp-dev (= 0.9.0+dfsg-5), libyaml-cpp0.9 (= 0.9.0+dfsg-5), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.4p1-1), openssh-common (= 1:10.4p1-1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), pci.ids (= 0.0~2026.07.06-1), perl (= 5.40.1-8), perl-base (= 5.40.1-8), perl-modules-5.40 (= 5.40.1-8), pkg-config (= 2.5.1-4), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), procps (= 2:4.0.6-2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261.1-3), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.10-0.1), util-linux (= 2.42.2-2), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1784059863" +------------------------------------------------------------------------------+ | Package contents Tue, 21 Jul 2026 10:56:54 +0000 | +------------------------------------------------------------------------------+ iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 122127244 bytes: control archive=700 bytes. 486 bytes, 12 lines control 402 bytes, 4 lines md5sums Package: iqtree3-dbgsym Source: iqtree3 (3.1.1+dfsg-2) Version: 3.1.1+dfsg-2+b1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 129241 Depends: iqtree3 (= 3.1.1+dfsg-2+b1) Section: debug Priority: optional Description: debug symbols for iqtree3 Build-Ids: 8eaea56b073c8f7ab472efebb496da9a2c2fd720 c873d9501c24346ecde944f7b7fc5f0c825c02c0 ca972a669a65cb319d553e01bcfbaa7ff7a0509c drwxr-xr-x root/root 0 2026-07-14 20:11 ./ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.build-id/8e/ -rw-r--r-- root/root 38657888 2026-07-14 20:11 ./usr/lib/debug/.build-id/8e/aea56b073c8f7ab472efebb496da9a2c2fd720.debug drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.build-id/c8/ -rw-r--r-- root/root 38250448 2026-07-14 20:11 ./usr/lib/debug/.build-id/c8/73d9501c24346ecde944f7b7fc5f0c825c02c0.debug drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.build-id/ca/ -rw-r--r-- root/root 38250480 2026-07-14 20:11 ./usr/lib/debug/.build-id/ca/972a669a65cb319d553e01bcfbaa7ff7a0509c.debug drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 17168504 2026-07-14 20:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree3.debug drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/share/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-07-14 20:11 ./usr/share/doc/iqtree3-dbgsym -> iqtree3 iqtree3_3.1.1+dfsg-2+b1_amd64.deb --------------------------------- new Debian package, version 2.0. size 10723328 bytes: control archive=2396 bytes. 3246 bytes, 61 lines control 1196 bytes, 17 lines md5sums Package: iqtree3 Source: iqtree3 (3.1.1+dfsg-2) Version: 3.1.1+dfsg-2+b1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 36215 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.9 (>= 0.7.0), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://www.iqtree.org Description: efficient phylogenetic software by maximum likelihood; 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 2026-07-14 20:11 ./ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/bin/ -rwxr-xr-x root/root 11513176 2026-07-14 20:11 ./usr/bin/iqtree3 -rwxr-xr-x root/root 11607384 2026-07-14 20:11 ./usr/bin/iqtree3-mpi -rwxr-xr-x root/root 11513176 2026-07-14 20:11 ./usr/bin/iqtree3-omp drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/share/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./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 230 2026-07-14 20:11 ./usr/share/doc/iqtree3/changelog.Debian.amd64.gz -rw-r--r-- root/root 987 2026-07-14 20:11 ./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 2026-07-14 20:11 ./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 2026-07-14 20:11 ./usr/share/man/ drwxr-xr-x root/root 0 2026-07-14 20:11 ./usr/share/man/man1/ -rw-r--r-- root/root 7277 2026-07-14 20:11 ./usr/share/man/man1/iqtree3-mpi.1.gz -rw-r--r-- root/root 7275 2026-07-14 20:11 ./usr/share/man/man1/iqtree3-omp.1.gz -rw-r--r-- root/root 7255 2026-07-14 20:11 ./usr/share/man/man1/iqtree3.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 21 Jul 2026 10:56:56 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 21 Jul 2026 10:56:56 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 21 Jul 2026 10:56:58 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3518716 Build-Time: 919 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdKT9Ddd/inputs/iqtree3_3.1.1+dfsg-2.dsc Machine Architecture: amd64 Package: iqtree3 Package-Time: 931 Source-Version: 3.1.1+dfsg-2 Space: 3518716 Status: successful Version: 3.1.1+dfsg-2+b1 -------------------------------------------------------------------------------- Finished at 2026-07-21T10:56:52Z Build needed 00:15:31, 3518716k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdKT9Ddd/out checking iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb: size differs for iqtree3-dbgsym_3.1.1+dfsg-2+b1_amd64.deb