=============================================================================== 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/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2_amd64.buildinfo Source: iqtree Version: 2.4.0+dfsg-2 rebuilderd-worker node: osuosl41-amd64 +------------------------------------------------------------------------------+ | Downloading sources Wed, 10 Jun 2026 02:47:52 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [151 kB] Get:7 https://deb.debian.org/debian sid InRelease [189 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [174 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [83.0 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [262 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3,220 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8,544 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.9 MB] Get:19 https://deb.debian.org/debian sid/main Sources [11.5 MB] Get:20 https://deb.debian.org/debian sid/non-free-firmware Sources [10.8 kB] Get:21 https://deb.debian.org/debian experimental/main Sources [400 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 34.6 MB in 4s (9,136 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg-2.dsc' iqtree_2.4.0+dfsg-2.dsc 2177 SHA256:35b9063fdc325c91918e90235c26c49937791f79f4e7ff177bbaabfe15855654 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg.orig.tar.xz' iqtree_2.4.0+dfsg.orig.tar.xz 2291260 SHA256:cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg-2.debian.tar.xz' iqtree_2.4.0+dfsg-2.debian.tar.xz 22260 SHA256:b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e iqtree_2.4.0+dfsg.orig.tar.xz b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 iqtree_2.4.0+dfsg-2.debian.tar.xz 35b9063fdc325c91918e90235c26c49937791f79f4e7ff177bbaabfe15855654 iqtree_2.4.0+dfsg-2.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Wed, 10 Jun 2026 02:47:57 +0000 | +------------------------------------------------------------------------------+ Rebuilding iqtree=2.4.0+dfsg-2 in /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdH4QLUQ/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/iqtree-2.4.0+dfsg I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [189 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 Packages [10.5 MB] Fetched 10.7 MB in 1s (7549 kB/s) Reading package lists... Get:1 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.46-3 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdr9dhulg/libctf0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260302-1 [142 kB] Fetched 142 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpai8kdwuu/mawk_1.3.4.20260302-1_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/tmpfondc_po/libsasl2-modules-db_2.1.28+dfsg1-11_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp37o3m3nf/libprrte3_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b2 [880 kB] Fetched 880 kB in 0s (71.1 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp5c53ndtj/procps_4.0.4-9+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-17 [2780 kB] Fetched 2780 kB in 0s (132 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjp5_nktz/libstdc++-15-dev_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.26-1 [2311 kB] Fetched 2311 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1bmjilup/gettext_0.26-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdf3gljvb/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpukdtgqpj/base-passwd_3.6.8_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2emify0/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (98.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_vagw95k/dpkg_1.23.7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b2 [66.3 kB] Fetched 66.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvgc_6ut1/libpam0g_1.7.0-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.32 [76.8 kB] Fetched 76.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9j5wbiin/libdebhelper-perl_13.32_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-17 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2sfdd8se/cpp-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-16 [1098 kB] Fetched 1098 kB in 0s (86.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyv3ivqyy/libc-gconv-modules-extra_2.42-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmphsopl2x8/libattr1_2.5.2-4_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 (58.5 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpf8ujyj9u/libgmp-dev_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpikvhkcjq/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmz_m7yvz/libevent-core-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Fetched 93.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7vxonnyr/libedit2_3.1-20260512-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp06b3oq_4/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2.1 [78.8 kB] Fetched 78.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpenoacdpi/libk5crypto3_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.7-1 [361 kB] Fetched 361 kB in 0s (4666 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8wi0c_l1/libarchive13t64_3.8.7-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt9m99ez2/dwz_0.16-4_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 (53.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzv8veedr/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-1 [28.3 kB] Fetched 28.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo3k2fvx9/libibumad3_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.2.0-2 [43.2 kB] Fetched 43.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpngg76bql/libmd0_1.2.0-2_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/tmpedto6qxc/libdebconfclient0_0.283_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/tmp1itpo3dx/ocl-icd-libopencl1_2.3.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4ph1wcy/libjs-jquery-ui_1.13.2+dfsg-1_all.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/tmp9mveyzi4/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Fetched 328 kB in 0s (0 B/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmphx4767ar/libgmpxx4ldbl_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Fetched 3504 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaq6jbi7r/mpi-default-dev_1.20_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcuy_alew/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsframe3 amd64 2.46-3 [84.7 kB] Fetched 84.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1cp70j0u/libsframe3_2.46-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmswzunjr/libxnvctrl0_535.171.04-1+b3_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 (7103 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwl6najuw/googletest_1.17.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.26-1 [315 kB] Fetched 315 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwr4cm76i/gettext-base_0.26-1_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/tmpdstd8rk3/libltdl7_2.5.4-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16.1.0-1 [2572 kB] Fetched 2572 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptr8ung_i/libtsan2_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-1 [43.0 kB] Fetched 43.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7vvdx3hr/libibmad5_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpubej4kz2/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Fetched 50.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpxd1t6ea_/libxext6_1.3.4-1+b4_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/tmpk04gkwe_/perl_5.40.1-8_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 (0 B/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpk_rdw0_0/libgmp10_6.3.0+dfsg-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42.1-3 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9u544hem/libsmartcols1_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2.1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpof3rfiwk/libgssapi-krb5-2_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 16.1.0-1 [148 kB] Fetched 148 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx60y2gtw/libquadmath0_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1+b1 [350 kB] Fetched 350 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcofz1ts5/libtinfo6_6.6+20251231-1+b1_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 (58.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdj7c10tk/libhsa-runtime64-1_6.4.3+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.6.2-1 [2482 kB] Fetched 2482 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp77nrsvlx/libssl3t64_3.6.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.10-1 [85.4 kB] Fetched 85.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa2bgsys8/libselinux1_3.10-1_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 (1705 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsx40050y/libsprng2-dev_2.0a-19_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b2 [175 kB] Fetched 175 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpejatjf3s/libpam-modules_1.7.0-5+b2_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/tmp16zr5sn5/libpkgconf7_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-1 [23.3 kB] Fetched 23.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphxkspk96/libdrm-amdgpu1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.46-3 [2632 kB] Fetched 2632 kB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnhzt1c1c/binutils-common_2.46-3_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 (95.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lvsu62x/dpkg-dev_1.23.7_all.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/tmpwi3jnky3/zlib1g_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-16 [622 kB] Fetched 622 kB in 0s (58.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp69kg9msa/libc-bin_2.42-16_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/tmpn9qdknxe/sysvinit-utils_3.18-1_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/tmp33u27_be/libuv1t64_1.52.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46-3 [1058 kB] Fetched 1058 kB in 0s (84.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphpgp_tcl/binutils-x86-64-linux-gnu_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-1 [62.6 kB] Fetched 62.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaeishtr6/libibverbs1_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-1 [7808 B] Fetched 7808 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt0tijf89/libdrm-common_2.4.134-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-16 [1996 kB] Fetched 1996 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_u0cb0e/libc6-dev_2.42-16_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/tmphwbof_w1/libnuma1_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16.1.0-1 [1136 kB] Fetched 1136 kB in 0s (86.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc1tpzsxb/libubsan1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42.1-3 [1226 kB] Fetched 1226 kB in 0s (90.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgrwb0qre/util-linux_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp-dev amd64 0.8.0+dfsg-9+b1 [170 kB] Fetched 170 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppcewg1uo/libyaml-cpp-dev_0.8.0+dfsg-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16.1.0-1 [2888 kB] Fetched 2888 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_v15b5c/libasan8_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpt00l5913/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 16.1.0-1 [46.1 kB] Fetched 46.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz4b6r4w2/libcc1-0_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-17 [23.4 MB] Fetched 23.4 MB in 0s (187 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoqh1vytf/gcc-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Fetched 61.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8kylzxgj/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_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/tmp7pg_qpd7/libmagic1t64_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-1 [383 kB] Fetched 383 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbuw6nm4/ibverbs-providers_63.0-1_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/tmp6cjpeg7e/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-16 [1789 kB] Fetched 1789 kB in 0s (108 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdx2xejie/libc6_2.42-16_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/tmpq1qz10jx/libboost-dev_1.90.0.2_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/tmp9_574o7g/gcc-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Fetched 80.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplwpeama7/libfido2-1_1.17.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess-dev amd64 0.17-3+b4 [55.5 kB] Fetched 55.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdhx6qqk5/libpciaccess-dev_0.17-3+b4_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 (138 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpewapitba/perl-modules-5.40_5.40.1-8_all.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 (74.4 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmp4zcv5zr0/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Fetched 35.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps5bu1mc0/pkgconf-bin_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 261~rc3-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk1aa2pkx/libudev1_261~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-4 [700 kB] Fetched 700 kB in 0s (63.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp830per0d/findutils_4.10.0-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-3 [820 kB] Fetched 820 kB in 0s (66.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyyphlm7r/libgprofng0_2.46-3_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/tmpp3l86rio/libcrypt1_4.5.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Fetched 345 kB in 0s (34.2 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.47-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpcs_4ocph/libmagic-mgc_5.47-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvwoek8o8/libnghttp3-9_1.15.0-1_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/tmpkfox_c1o/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.3-1 [16.2 MB] Fetched 16.2 MB in 2s (9255 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi81ixhd7/cmake_4.3.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-3 [244 kB] Fetched 244 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzc4xs9lq/libssh2-1t64_1.11.1-3_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/tmpng0ja3jp/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.20.0-5 [409 kB] Fetched 409 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphhfpb18r/libcurl4t64_8.20.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Fetched 516 kB in 0s (48.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfzw4gs55/autoconf_2.73-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-16 [37.9 kB] Fetched 37.9 kB in 0s (3400 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl5lxq87d/libc-dev-bin_2.42-16_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 (67.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpykmhm89t/libmpfr6_4.2.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.32 [933 kB] Fetched 933 kB in 0s (76.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ll1tu4a/debhelper_13.32_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1+b1 [442 kB] Fetched 442 kB in 0s (42.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgcnmnr5r/ncurses-bin_6.6+20251231-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16.1.0-1 [1281 kB] Fetched 1281 kB in 0s (93.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx_u5iiqh/liblsan0_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-17 [13.2 MB] Fetched 13.2 MB in 0s (154 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdcxtckmy/g++-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Fetched 59.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwhj_ve5q/libpsl5t64_0.21.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-1 [260 kB] Fetched 260 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpheqt7ptt/libhwloc-dev_2.14.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.4-1 [63.4 kB] Fetched 63.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi9yo83pc/rpcsvc-proto_1.4.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Fetched 28.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxuxrt1sm/libxdmcp6_1.1.5-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-17 [12.1 MB] Fetched 12.1 MB in 0s (165 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb_bh18_l/cpp-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Fetched 308 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ld7t7h0/libevent-dev_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-3 [548 kB] Fetched 548 kB in 0s (52.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttfr5_yz/libbinutils_2.46-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpezk3oe2q/libnghttp2-14_1.69.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp0.8 amd64 0.8.0+dfsg-9+b1 [130 kB] Fetched 130 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp55ncyxqm/libyaml-cpp0.8_0.8.0+dfsg-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261~rc3-1 [3498 kB] Fetched 3498 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp56an5wsh/systemd_261~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.134-1 [21.5 kB] Fetched 21.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdxghw_r6/libdrm-radeon1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b2 [188 kB] Fetched 188 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7svepmk7/libldap2_2.6.10+dfsg-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-8 [1677 kB] Fetched 1677 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp51sufjy6/perl-base_5.40.1-8_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/tmpqt0d7ygu/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-17 [36.8 kB] Fetched 36.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppoy9jf0g/gcc-15-base_15.2.0-17_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/tmpqinfcqof/libpsm2-2_11.2.185-2.1_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/tmp9xj33yf4/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5vzc038/libngtcp2-16_1.22.1-1_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/tmpnxj59toi/libnuma-dev_2.0.19-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-1 [166 kB] Fetched 166 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxewnp8cu/libhwloc15_2.14.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2.1 [30.9 kB] Fetched 30.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps5hq62hz/libkrb5support0_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b2 [77.7 kB] Fetched 77.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl71zmrj4/libgdbm6t64_1.26-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.3-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjrommxwb/liblzma5_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b2 [45.6 kB] Fetched 45.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9axh564l/libpam-modules-bin_1.7.0-5+b2_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/tmpzoem5eui/libpcre2-8-0_10.46-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-3 [331 kB] Fetched 331 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp79eexcsc/sed_4.9-3_amd64.deb' Downloading dependency 1 of 268: libctf0:amd64=2.46-3 Downloading dependency 2 of 268: mawk:amd64=1.3.4.20260302-1 Downloading dependency 3 of 268: libsasl2-modules-db:amd64=2.1.28+dfsg1-11 Downloading dependency 4 of 268: libprrte3:amd64=3.0.13-3 Downloading dependency 5 of 268: procps:amd64=2:4.0.4-9+b2 Downloading dependency 6 of 268: libstdc++-15-dev:amd64=15.2.0-17 Downloading dependency 7 of 268: 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dependency 23 of 268: libarchive13t64:amd64=3.8.7-1 Downloading dependency 24 of 268: dwz:amd64=0.16-4 Downloading dependency 25 of 268: libtool:amd64=2.5.4-11 Downloading dependency 26 of 268: libibumad3:amd64=63.0-1 Downloading dependency 27 of 268: libmd0:amd64=1.2.0-2 Downloading dependency 28 of 268: libdebconfclient0:amd64=0.283 Downloading dependency 29 of 268: ocl-icd-libopencl1:amd64=2.3.4-1+b1 Downloading dependency 30 of 268: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 31 of 268: grep:amd64=3.12-1 Downloading dependency 32 of 268: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-5+b2 Downloading dependency 33 of 268: mpi-default-dev:amd64=1.20 Downloading dependency 34 of 268: libjansson4:amd64=2.14-2+b4 Downloading dependency 35 of 268: libsframe3:amd64=2.46-3 Downloading dependency 36 of 268: libxnvctrl0:amd64=535.171.04-1+b3 Downloading dependency 37 of 268: googletest:amd64=1.17.0-1 Downloading dependency 38 of 268: gettext-base:amd64=0.26-1 Downloading dependency 39 of 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Downloading dependency 87 of 268: libudev1:amd64=261~rc3-1 Downloading dependency 88 of 268: findutils:amd64=4.10.0-4 Downloading dependency 89 of 268: libgprofng0:amd64=2.46-3 Downloading dependency 90 of 268: libcrypt1:amd64=1:4.5.1-1+b1 Downloading dependency 91 of 268: libmagic-mgc:amd64=1:5.47-4 Downloading dependency 92 of 268: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 93 of 268: build-essential:amd64=12.12 Downloading dependency 94 of 268: cmake:amd64=4.3.3-1 Downloading dependency 95 of 268: libssh2-1t64:amd64=1.11.1-3 Downloading dependency 96 of 268: patch:amd64=2.8-2 Downloading dependency 97 of 268: libcurl4t64:amd64=8.20.0-5 Downloading dependency 98 of 268: autoconf:amd64=2.73-2 Downloading dependency 99 of 268: libc-dev-bin:amd64=2.42-16 Downloading dependency 100 of 268: libmpfr6:amd64=4.2.2-3 Downloading dependency 101 of 268: debhelper:amd64=13.32 Downloading dependency 102 of 268: ncurses-bin:amd64=6.6+20251231-1+b1 Downloading dependency 103 of 268: liblsan0:amd64=16.1.0-1 Downloading dependency 104 of 268: g++-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 105 of 268: libpsl5t64:amd64=0.21.5-1 Downloading dependency 106 of 268: libhwloc-dev:amd64=2.14.0-1 Downloading dependency 107 of 268: rpcsvc-proto:amd64=1.4.4-1 Downloading dependency 108 of 268: libxdmcp6:amd64=1:1.1.5-2+b1 Downloading dependency 109 of 268: cpp-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 110 of 268: libevent-dev:amd64=2.1.12-stable-10+b2 Downloading dependency 111 of 268: libbinutils:amd64=2.46-3 Downloading dependency 112 of 268: libnghttp2-14:amd64=1.69.0-1 Downloading dependency 113 of 268: libyaml-cpp0.8:amd64=0.8.0+dfsg-9+b1 Downloading dependency 114 of 268: systemd:amd64=261~rc3-1 Downloading dependency 115 of 268: libdrm-radeon1:amd64=2.4.134-1 Downloading dependency 116 of 268: libldap2:amd64=2.6.10+dfsg-1+b2 Downloading dependency 117 of 268: perl-base:amd64=5.40.1-8 Downloading dependency 118 of 268: autotools-dev:amd64=20240727.1+nmu1 Downloading dependency 119 of 268: gcc-15-base:amd64=15.2.0-17 Downloading dependency 120 of 268: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 121 of 268: openmpi-bin:amd64=5.0.10-1 Downloading dependency 122 of 268: libngtcp2-16:amd64=1.22.1-1 Downloading dependency 123 of 268: libnuma-dev:amd64=2.0.19-1+b2 Downloading dependency 124 of 268: libhwloc15:amd64=2.14.0-1 Downloading dependency 125 of 268: libkrb5support0:amd64=1.22.1-2.1 Downloading dependency 126 of 268: libgdbm6t64:amd64=1.26-1+b2 Downloading dependency 127 of 268: liblzma5:amd64=5.8.3-1 Downloading dependency 128 of 268: libpam-modules-bin:amd64=1.7.0-5+b2 Downloading dependency 129 of 268: libpcre2-8-0:amd64=10.46-1+b2 Downloading dependency 130 of 268: sed:amd64=4.9-3 Downloading dependency 131 of 268: libgcc-s1:amd64=16.1.0-1Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 16.1.0-1 [74.0 kB] Fetched 74.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp03fivh9/libgcc-s1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_n2u6d_a/intltool-debian_0.35.0+20060710.6_all.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 (172 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps7nyufdp/libz3-4_4.13.3-1.1_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/tmpooxlc1wi/bzip2_1.0.8-6+b2_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/tmpdztiardb/gcc_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Fetched 642 kB in 0s (60.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw9gmpci9/libxml2-16_2.15.3+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5+b1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp6q843tsi/g++_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42.1-3 [33.3 kB] Fetched 33.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkw792974/libuuid1_2.42.1-3_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 (179 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7seofuh8/libboost1.90-dev_1.90.0-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-1 [878 kB] Fetched 878 kB in 0s (69.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphc73x8c6/libgfortran5_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 7.0.10-1 [1994 kB] Fetched 1994 kB in 0s (80.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqay3pum2/linux-libc-dev_7.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Fetched 6020 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiju8ghbr/dh-strip-nondeterminism_1.15.1-1_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 (91.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7wd78f09/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-1 [71.7 kB] Fetched 71.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzim31it1/librdmacm1t64_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-3 [1559 kB] Fetched 1559 kB in 0s (81.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcqeiby2o/bash_5.3-3_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 (170 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjmtse7tp/libamd-comgr3_7.0.2+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.3-1 [17.9 kB] Fetched 17.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4twzmpe3/libcap-ng0_0.9.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.134-1 [19.3 kB] Fetched 19.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcykx089k/libdrm-nouveau2_2.4.134-1_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/tmpbvmqpsuf/libfuse3-4_3.18.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.7.0~rc1-1 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw314o03q/libucc1_1.7.0~rc1-1_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/tmptc6klcvn/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (61.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7kd1bpln/libisl23_0.27-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b2 [27.1 kB] Fetched 27.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfqmr1wu1/libxxhash0_0.8.3-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-1 [695 kB] Fetched 695 kB in 0s (58.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpao_9nplw/libibverbs-dev_63.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-3 [282 kB] Fetched 282 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnlf51m58/binutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-17 [20.8 kB] Fetched 20.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3nlazlw5/gfortran-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.3p1-4 [1003 kB] Fetched 1003 kB in 0s (76.6 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.3p1-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp6xybxijb/openssh-client_10.3p1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-1 [38.5 kB] Fetched 38.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9yedv91l/libdrm2_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg27atphv/po-debconf_1.0.22_all.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/tmp9n6wz7i5/libbsd0_0.12.2-3_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/tmpukwion77/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjjm7zkd/libpam-runtime_1.7.0-5_all.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 (13.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7kun0pmr/libeigen3-dev_3.4.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 time amd64 1.10-0.1 [58.4 kB] Fetched 58.4 kB in 0s (3231 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpewae6uko/time_1.10-0.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.26-1 [802 kB] Fetched 802 kB in 0s (47.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1bq1ygw9/autopoint_0.26-1_all.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/tmplnzekq6q/libcom-err2_1.47.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Fetched 500 kB in 0s (8971 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm1u5ybte/libsimde-dev_0.8.4~rc3-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16.1.0-1 [1580 kB] Fetched 1580 kB in 0s (101 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_g3pjjeg/libhwasan0_16.1.0-1_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 (99.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19wme_2i/libopenmpi40_5.0.10-1_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/tmpn8y_lcsa/libprrte-bin_3.0.13-3_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 (66.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4s4iexan/libfabric1_2.1.0-1.1+b2_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/tmpeheyvlxh/libgdbm-compat4t64_1.26-1+b2_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/tmpmg938lv2/libltdl-dev_2.5.4-11_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/tmpy3qh0n5t/libsasl2-2_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.42.1-3 [164 kB] Fetched 164 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyjf4d5mn/mount_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp9_h_sy16/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-smi26 amd64 7.2.0-3 [830 kB] Fetched 830 kB in 0s (73.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyhwsgja2/libamd-smi26_7.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 16.1.0-1 [10.4 kB] Fetched 10.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpijjzsclo/libatomic1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk5q7bg2o/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Fetched 18.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp9ie5rbj/libmunge2_0.5.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2.1 [335 kB] Fetched 335 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_fzq33_f/libkrb5-3_1.22.1-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-17 [542 kB] Fetched 542 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7to6llnn/gcc-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Fetched 1028 kB in 0s (83.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdp_7_zh6/libopenmpi-dev_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1+b1 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpllfew23v/libncursesw6_6.6+20251231-1+b1_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 (829 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr07b12u_/librhash1_1.4.6-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-1 [24.7 kB] Fetched 24.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9iog2ly6/libhwloc-plugins_2.14.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (0 B/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmpfduq60tr/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [4644 B] Fetched 4644 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7zdcoi0a/cpp-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261~rc3-1 [2561 kB] Fetched 2561 kB in 0s (104 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoihpluvd/libsystemd-shared_261~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-17 [886 kB] Fetched 886 kB in 0s (76.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4w80z23/libgfortran-15-dev_15.2.0-17_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 (72.6 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp6o05fs3m/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-17 [2718 kB] Fetched 2718 kB in 0s (135 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpig81s7p5/libgcc-15-dev_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.1-3 [99.7 kB] Fetched 99.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfw1_12rm/bsdextrautils_2.42.1-3_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/tmpnn07_czd/libnl-route-3-200_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Fetched 220 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp3f7bvb_/libnl-route-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Fetched 54.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnk3gf3o1/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_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/tmp9el0a7xi/libxcb1_1.17.0-2+b2_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 (1892 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_yyafax8/libsprng2_2.0a-19_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/tmpe9pe605w/sensible-utils_0.0.26_all.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 (178 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdga2u4ck/libamdhip64-6_6.4.3-5_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/tmpj02wk46b/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9xjohld6/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_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/tmpum62alys/cpp_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Fetched 52.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpszvkvtkb/libpciaccess0_0.17-3+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Fetched 20.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp8v1jt5em/libxau6_1.0.11-1+b2_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/tmplh67ss4q/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps1k5rsx8/libfile-stripnondeterminism-perl_1.15.1-1_all.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/tmpo4a_xfiy/libidn2-0_2.3.8-5_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/tmpjir98roe/libbz2-1.0_1.0.8-6+b2_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/tmpp0hrf0t8/init-system-helpers_1.69_all.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/tmp2w689wmh/libuchardet0_0.0.8-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-10 [14.9 kB] Fetched 14.9 kB in 0s (422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8cft2yww/liblocale-gettext-perl_1.07-10_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 (155 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ht08p9b/libperl5.40_5.40.1-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.1-1 [117 kB] Fetched 117 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpifu0d2et/libexpat1_2.8.1-1_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/tmpu4fccqfr/libmpc3_1.3.1-3_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 (69.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppixui06e/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt1mch1kq/ncurses-base_6.6+20251231-1_all.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/tmp_6q3ecyy/file_5.47-4_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/tmpxj9664ow/debianutils_5.23.2_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 (94.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprt_nisj4/groff-base_1.24.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b1 [767 kB] Fetched 767 kB in 0s (63.5 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpyskyptc2/libclang-common-21-dev_21.1.8-7+b1_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 (66.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2dcnyanq/libdb5.3t64_5.3.28+dfsg2-11+b1_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 (98.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkacdwe0g/libprrte-dev_3.0.13-3_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 (77.9 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp2uze37yk/zlib1g-dev_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 16.1.0-1 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjvhy8m3t/libgomp1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0px43f8o/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.7-2 [86.5 kB] Fetched 86.5 kB in 0s (4675 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz5ip4o7o/libjsoncpp26_1.9.7-2_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/tmp82lvoj5z/libnettle8t64_3.10.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.3-1 [740 kB] Fetched 740 kB in 0s (66.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsbfuj1ea/xz-utils_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-17 [28.0 kB] Fetched 28.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_yh4y6dr/g++-15_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-3 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpokly63d1/libctf-nobfd0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplw04e4qc/coreutils_9.10-1_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/tmp2ktm6k74/libbrotli1_1.2.0-3_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 (62.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkm86oyn9/libdpkg-perl_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.134-1 [64.1 kB] Fetched 64.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvcjfc776/libdrm-intel1_2.4.134-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b1 [28.2 MB] Fetched 28.2 MB in 0s (182 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpwuz9dqpc/libllvm21_21.1.8-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Fetched 49.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkkeh4az4/libpipeline1_1.5.8-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.20.1-1 [954 kB] Fetched 954 kB in 0s (78.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6nskt_mp/libucx0_1.20.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB] Fetched 23.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgc9y2niw/libngtcp2-crypto-ossl0_1.22.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.6.2-1 [316 kB] Fetched 316 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu0qi8cyx/openssl-provider-legacy_3.6.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-dev amd64 2.4.134-1 [305 kB] Fetched 305 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjidrjrcf/libdrm-dev_2.4.134-1_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 (1842 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbd_qprsv/liblz4-1_1.10.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b1 [670 kB] Fetched 670 kB in 0s (59.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpltng97he/libpmix2t64_6.0.0+really5.0.9-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 261~rc3-1 [467 kB] Fetched 467 kB in 0s (46.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgc7sge18/libsystemd0_261~rc3-1_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/tmpq3bjyglw/g++-x86-64-linux-gnu_15.2.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-4 [25.2 kB] Fetched 25.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssj7nstg/libffi8_3.5.2-4_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/tmp085oketm/base-files_14.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42.1-3 [213 kB] Fetched 213 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9k68vi4w/libmount1_2.42.1-3_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/tmpme6kssrj/libzstd1_1.5.7+dfsg-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Fetched 58.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpemc0hyuq/libelf1t64_0.195-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-17 [12.8 MB] Fetched 12.8 MB in 0s (187 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6d1eg81h/gfortran-15-x86-64-linux-gnu_15.2.0-17_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Fetched 184 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcrdsox7h/libevent-2.1-7t64_2.1.12-stable-10+b2_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/tmpafcaj6f2/debconf_1.5.92_all.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/tmpgr66jb30/libnl-3-200_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 16.1.0-1 [823 kB] Fetched 823 kB in 0s (72.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphsucd0gu/libstdc++6_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-16-base amd64 16.1.0-1 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_m9izaro/gcc-16-base_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42.1-3 [172 kB] Fetched 172 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpedbyv5vv/libblkid1_2.42.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b2 [63.8 kB] Fetched 63.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpafvj8yv_/libproc2-0_4.0.4-9+b2_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/tmpw5v76627/gzip_1.13-1_amd64.deb' Downloading dependency 132 of 268: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 133 of 268: libz3-4:amd64=4.13.3-1.1 Downloading dependency 134 of 268: bzip2:amd64=1.0.8-6+b2 Downloading dependency 135 of 268: gcc:amd64=4:15.2.0-5+b1 Downloading dependency 136 of 268: libxml2-16:amd64=2.15.3+dfsg-1 Downloading dependency 137 of 268: g++:amd64=4:15.2.0-5+b1 Downloading dependency 138 of 268: libuuid1:amd64=2.42.1-3 Downloading dependency 139 of 268: libboost1.90-dev:amd64=1.90.0-6 Downloading dependency 140 of 268: libgfortran5:amd64=16.1.0-1 Downloading dependency 141 of 268: linux-libc-dev:amd64=7.0.10-1 Downloading dependency 142 of 268: dh-strip-nondeterminism:amd64=1.15.1-1 Downloading dependency 143 of 268: man-db:amd64=2.13.1-1 Downloading dependency 144 of 268: librdmacm1t64:amd64=63.0-1 Downloading dependency 145 of 268: bash:amd64=5.3-3 Downloading dependency 146 of 268: libamd-comgr3:amd64=7.0.2+dfsg-3 Downloading dependency 147 of 268: libcap-ng0:amd64=0.9.3-1 Downloading dependency 148 of 268: libdrm-nouveau2:amd64=2.4.134-1 Downloading dependency 149 of 268: libfuse3-4:amd64=3.18.2-2 Downloading dependency 150 of 268: libucc1:amd64=1.7.0~rc1-1 Downloading dependency 151 of 268: hostname:amd64=3.25 Downloading dependency 152 of 268: libisl23:amd64=0.27-2 Downloading dependency 153 of 268: libxxhash0:amd64=0.8.3-2+b2 Downloading dependency 154 of 268: libibverbs-dev:amd64=63.0-1 Downloading dependency 155 of 268: binutils:amd64=2.46-3 Downloading dependency 156 of 268: gfortran-15:amd64=15.2.0-17 Downloading dependency 157 of 268: openssh-client:amd64=1:10.3p1-4 Downloading dependency 158 of 268: libdrm2:amd64=2.4.134-1 Downloading dependency 159 of 268: po-debconf:amd64=1.0.22 Downloading dependency 160 of 268: libbsd0:amd64=0.12.2-3 Downloading dependency 161 of 268: dash:amd64=0.5.12-12 Downloading dependency 162 of 268: libpam-runtime:amd64=1.7.0-5 Downloading dependency 163 of 268: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 164 of 268: time:amd64=1.10-0.1 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libmunge2:amd64=0.5.18-1 Downloading dependency 181 of 268: libkrb5-3:amd64=1.22.1-2.1 Downloading dependency 182 of 268: gcc-15:amd64=15.2.0-17 Downloading dependency 183 of 268: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 184 of 268: libncursesw6:amd64=6.6+20251231-1+b1 Downloading dependency 185 of 268: librhash1:amd64=1.4.6-1.1+b1 Downloading dependency 186 of 268: libhwloc-plugins:amd64=2.14.0-1 Downloading dependency 187 of 268: libx11-data:amd64=2:1.8.13-1 Downloading dependency 188 of 268: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 189 of 268: libsystemd-shared:amd64=261~rc3-1 Downloading dependency 190 of 268: libgfortran-15-dev:amd64=15.2.0-17 Downloading dependency 191 of 268: libx11-6:amd64=2:1.8.13-1 Downloading dependency 192 of 268: libgcc-15-dev:amd64=15.2.0-17 Downloading dependency 193 of 268: bsdextrautils:amd64=2.42.1-3 Downloading dependency 194 of 268: libnl-route-3-200:amd64=3.12.0-2+b1 Downloading dependency 195 of 268: libnl-route-3-dev:amd64=3.12.0-2+b1 Downloading dependency 196 of 268: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 197 of 268: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 198 of 268: libsprng2:amd64=2.0a-19 Downloading dependency 199 of 268: sensible-utils:amd64=0.0.26 Downloading dependency 200 of 268: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 201 of 268: m4:amd64=1.4.21-1 Downloading dependency 202 of 268: libevent-extra-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 203 of 268: cpp:amd64=4:15.2.0-5+b1 Downloading dependency 204 of 268: libpciaccess0:amd64=0.17-3+b4 Downloading dependency 205 of 268: libxau6:amd64=1:1.0.11-1+b2 Downloading dependency 206 of 268: dh-autoreconf:amd64=22 Downloading dependency 207 of 268: libfile-stripnondeterminism-perl:amd64=1.15.1-1 Downloading dependency 208 of 268: libidn2-0:amd64=2.3.8-5 Downloading dependency 209 of 268: libbz2-1.0:amd64=1.0.8-6+b2 Downloading dependency 210 of 268: init-system-helpers:amd64=1.69 Downloading dependency 211 of 268: libuchardet0:amd64=0.0.8-2+b2 Downloading dependency 212 of 268: liblocale-gettext-perl:amd64=1.07-10 Downloading dependency 213 of 268: libperl5.40:amd64=5.40.1-8 Downloading dependency 214 of 268: libexpat1:amd64=2.8.1-1 Downloading dependency 215 of 268: libmpc3:amd64=1.3.1-3 Downloading dependency 216 of 268: tar:amd64=1.35+dfsg-4 Downloading dependency 217 of 268: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 218 of 268: file:amd64=1:5.47-4 Downloading dependency 219 of 268: debianutils:amd64=5.23.2 Downloading dependency 220 of 268: groff-base:amd64=1.24.1-1 Downloading dependency 221 of 268: libclang-common-21-dev:amd64=1:21.1.8-7+b1 Downloading dependency 222 of 268: libdb5.3t64:amd64=5.3.28+dfsg2-11+b1 Downloading dependency 223 of 268: libprrte-dev:amd64=3.0.13-3 Downloading dependency 224 of 268: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 225 of 268: libgomp1:amd64=16.1.0-1 Downloading dependency 226 of 268: libacl1:amd64=2.3.2-3 Downloading dependency 227 of 268: libjsoncpp26:amd64=1.9.7-2 Downloading dependency 228 of 268: libnettle8t64:amd64=3.10.2-1+b1 Downloading dependency 229 of 268: xz-utils:amd64=5.8.3-1 Downloading dependency 230 of 268: g++-15:amd64=15.2.0-17 Downloading dependency 231 of 268: libctf-nobfd0:amd64=2.46-3 Downloading dependency 232 of 268: coreutils:amd64=9.10-1 Downloading dependency 233 of 268: libbrotli1:amd64=1.2.0-3 Downloading dependency 234 of 268: libdpkg-perl:amd64=1.23.7 Downloading dependency 235 of 268: libdrm-intel1:amd64=2.4.134-1 Downloading dependency 236 of 268: libllvm21:amd64=1:21.1.8-7+b1 Downloading dependency 237 of 268: libpipeline1:amd64=1.5.8-3 Downloading dependency 238 of 268: libucx0:amd64=1.20.1-1 Downloading dependency 239 of 268: libngtcp2-crypto-ossl0:amd64=1.22.1-1 Downloading dependency 240 of 268: openssl-provider-legacy:amd64=3.6.2-1 Downloading dependency 241 of 268: libdrm-dev:amd64=2.4.134-1 Downloading dependency 242 of 268: liblz4-1:amd64=1.10.0-10 Downloading dependency 243 of 268: libpmix2t64:amd64=6.0.0+really5.0.9-3+b1 Downloading dependency 244 of 268: libsystemd0:amd64=261~rc3-1 Downloading dependency 245 of 268: g++-x86-64-linux-gnu:amd64=4:15.2.0-5+b1 Downloading dependency 246 of 268: libffi8:amd64=3.5.2-4 Downloading dependency 247 of 268: base-files:amd64=14.2 Downloading dependency 248 of 268: libmount1:amd64=2.42.1-3 Downloading dependency 249 of 268: libzstd1:amd64=1.5.7+dfsg-3+b2 Downloading dependency 250 of 268: libelf1t64:amd64=0.195-1 Downloading dependency 251 of 268: gfortran-15-x86-64-linux-gnu:amd64=15.2.0-17 Downloading dependency 252 of 268: libevent-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 253 of 268: debconf:amd64=1.5.92 Downloading dependency 254 of 268: libnl-3-200:amd64=3.12.0-2+b1 Downloading dependency 255 of 268: libstdc++6:amd64=16.1.0-1 Downloading dependency 256 of 268: gcc-16-base:amd64=16.1.0-1 Downloading dependency 257 of 268: libblkid1:amd64=2.42.1-3 Downloading dependency 258 of 268: libproc2-0:amd64=2:4.0.4-9+b2 Downloading dependency 259 of 268: gzip:amd64=1.13-1 Downloading dependency 260 of 268: libunistring5:amd64=1.4.2-1Get: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/tmpkjt14unq/libunistring5_1.4.2-1_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 (798 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy9ret8oc/pkg-config_2.5.1-4_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 (65.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfo4k9h7r/libze1_1.28.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 16.1.0-1 [27.0 kB] Fetched 27.0 kB in 0s (2566 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplju_dv4k/libitm1_16.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (6073 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5apfen23/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Fetched 9348 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qn8nlhj/libkeyutils1_1.6.3-6+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/tmpgv1i95d3/libcbor0.10_0.10.2-2.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2+b1 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp18_1cczg/libnl-3-dev_3.12.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Fetched 13.5 kB in 0s (727 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi1to5ffa/chrpath_0.18-1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpy_y4qu5c/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.lD3Y_t7w_E as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.lD3Y_t7w_E 127.0.0.1 - - [10/Jun/2026 02:49:39] code 404, message File not found 127.0.0.1 - - [10/Jun/2026 02:49:39] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:38515 ./ InRelease 127.0.0.1 - - [10/Jun/2026 02:49:39] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:38515 ./ Release [462 B] 127.0.0.1 - - [10/Jun/2026 02:49:39] code 404, message File not found 127.0.0.1 - - [10/Jun/2026 02:49:39] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:38515 ./ Release.gpg 127.0.0.1 - - [10/Jun/2026 02:49:39] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:38515 ./ Packages [329 kB] Fetched 330 kB in 0s (22.3 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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I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.lD3Y_t7w_E 127.0.0.1 - - [10/Jun/2026 02:49:40] code 404, message File not found 127.0.0.1 - - [10/Jun/2026 02:49:40] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:38515 ./ InRelease 127.0.0.1 - - [10/Jun/2026 02:49:40] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:38515 ./ Release 127.0.0.1 - - [10/Jun/2026 02:49:40] code 404, message File not found 127.0.0.1 - - [10/Jun/2026 02:49:40] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:38515 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... 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127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./googletest_1.17.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libpkgconf7_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./pkgconf-bin_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./pkgconf_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libsprng2_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libsprng2-dev_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libyaml-cpp0.8_0.8.0%2bdfsg-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libyaml-cpp-dev_0.8.0%2bdfsg-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libboost1.90-dev_1.90.0-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libboost-dev_1.90.0.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libeigen3-dev_3.4.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./time_1.10-0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [10/Jun/2026 02:50:21] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpy_y4qu5c/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.lD3Y_t7w_E Reading package lists... Building dependency tree... Reading state information... libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. mawk is already the newest version (1.3.4.20260302-1). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. procps is already the newest version (2:4.0.4-9+b2). procps set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-17). libstdc++-15-dev set to manually installed. gettext is already the newest version (0.26-1). gettext set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. base-passwd is already the newest version (3.6.8). make is already the newest version (4.4.1-3). make set to manually installed. dpkg is already the newest version (1.23.7). libpam0g is already the newest version (1.7.0-5+b2). libdebhelper-perl is already the newest version (13.32). libdebhelper-perl set to manually installed. cpp-15 is already the newest version (15.2.0-17). cpp-15 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-16). libattr1 is already the newest version (1:2.5.2-4). libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b2). libgmp-dev set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-core-2.1-7t64 set to manually installed. libedit2 is already the newest version (3.1-20260512-1). libedit2 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. libk5crypto3 is already the newest version (1.22.1-2.1). libk5crypto3 set to manually installed. libarchive13t64 is already the newest version (3.8.7-1). libarchive13t64 set to manually installed. dwz is already the newest version (0.16-4). dwz set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. libibumad3 is already the newest version (63.0-1). libibumad3 set to manually installed. libmd0 is already the newest version (1.2.0-2). libdebconfclient0 is already the newest version (0.283). ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. grep is already the newest version (3.12-1). libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b2). libgmpxx4ldbl set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. libsframe3 is already the newest version (2.46-3). libsframe3 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. googletest is already the newest version (1.17.0-1). googletest set to manually installed. gettext-base is already the newest version (0.26-1). gettext-base set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. libtsan2 is already the newest version (16.1.0-1). libtsan2 set to manually installed. libibmad5 is already the newest version (63.0-1). libibmad5 set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. perl is already the newest version (5.40.1-8). perl set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b2). libsmartcols1 is already the newest version (2.42.1-3). libgssapi-krb5-2 is already the newest version (1.22.1-2.1). libgssapi-krb5-2 set to manually installed. libquadmath0 is already the newest version (16.1.0-1). libquadmath0 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1+b1). libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libssl3t64 is already the newest version (3.6.2-1). libselinux1 is already the newest version (3.10-1). libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. libpam-modules is already the newest version (1.7.0-5+b2). libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.134-1). libdrm-amdgpu1 set to manually installed. binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libc-bin is already the newest version (2.42-16). sysvinit-utils is already the newest version (3.18-1). libuv1t64 is already the newest version (1.52.1-4). libuv1t64 set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46-3). binutils-x86-64-linux-gnu set to manually installed. libibverbs1 is already the newest version (63.0-1). libibverbs1 set to manually installed. libdrm-common is already the newest version (2.4.134-1). libdrm-common set to manually installed. libc6-dev is already the newest version (2.42-16). libc6-dev set to manually installed. libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. libubsan1 is already the newest version (16.1.0-1). libubsan1 set to manually installed. util-linux is already the newest version (2.42.1-3). libyaml-cpp-dev is already the newest version (0.8.0+dfsg-9+b1). libyaml-cpp-dev set to manually installed. libasan8 is already the newest version (16.1.0-1). libasan8 set to manually installed. diffutils is already the newest version (1:3.12-1). libcc1-0 is already the newest version (16.1.0-1). libcc1-0 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-17). gcc-15-x86-64-linux-gnu set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-openssl-2.1-7t64 set to manually installed. libmagic1t64 is already the newest version (1:5.47-4). libmagic1t64 set to manually installed. ibverbs-providers is already the newest version (63.0-1). ibverbs-providers set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libc6 is already the newest version (2.42-16). libboost-dev is already the newest version (1.90.0.2). libboost-dev 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. libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. libpciaccess-dev is already the newest version (0.17-3+b4). libpciaccess-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. automake is already the newest version (1:1.18.1-4). automake set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. libudev1 is already the newest version (261~rc3-1). findutils is already the newest version (4.10.0-4). libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). libmagic-mgc is already the newest version (1:5.47-4). libmagic-mgc set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. cmake is already the newest version (4.3.3-1). cmake set to manually installed. libssh2-1t64 is already the newest version (1.11.1-3). libssh2-1t64 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. libcurl4t64 is already the newest version (8.20.0-5). libcurl4t64 set to manually installed. autoconf is already the newest version (2.73-2). autoconf set to manually installed. libc-dev-bin is already the newest version (2.42-16). libc-dev-bin set to manually installed. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. debhelper is already the newest version (13.32). debhelper set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1+b1). liblsan0 is already the newest version (16.1.0-1). liblsan0 set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.2.0-17). g++-15-x86-64-linux-gnu set to manually installed. libpsl5t64 is already the newest version (0.21.5-1). libpsl5t64 set to manually installed. libhwloc-dev is already the newest version (2.14.0-1). libhwloc-dev set to manually installed. rpcsvc-proto is already the newest version (1.4.4-1). rpcsvc-proto set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-17). cpp-15-x86-64-linux-gnu set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. libyaml-cpp0.8 is already the newest version (0.8.0+dfsg-9+b1). libyaml-cpp0.8 set to manually installed. systemd is already the newest version (261~rc3-1). systemd set to manually installed. libdrm-radeon1 is already the newest version (2.4.134-1). libdrm-radeon1 set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b2). libldap2 set to manually installed. perl-base is already the newest version (5.40.1-8). autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. gcc-15-base is already the newest version (15.2.0-17). gcc-15-base set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. libhwloc15 is already the newest version (2.14.0-1). libhwloc15 set to manually installed. libkrb5support0 is already the newest version (1.22.1-2.1). libkrb5support0 set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. liblzma5 is already the newest version (5.8.3-1). libpam-modules-bin is already the newest version (1.7.0-5+b2). libpcre2-8-0 is already the newest version (10.46-1+b2). sed is already the newest version (4.9-3). libgcc-s1 is already the newest version (16.1.0-1). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libz3-4 is already the newest version (4.13.3-1.1). libz3-4 set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. gcc is already the newest version (4:15.2.0-5+b1). gcc set to manually installed. libxml2-16 is already the newest version (2.15.3+dfsg-1). libxml2-16 set to manually installed. g++ is already the newest version (4:15.2.0-5+b1). g++ set to manually installed. libuuid1 is already the newest version (2.42.1-3). libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libgfortran5 is already the newest version (16.1.0-1). libgfortran5 set to manually installed. linux-libc-dev is already the newest version (7.0.10-1). linux-libc-dev set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.1-1). dh-strip-nondeterminism set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. librdmacm1t64 is already the newest version (63.0-1). librdmacm1t64 set to manually installed. bash is already the newest version (5.3-3). libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. libcap-ng0 is already the newest version (0.9.3-1). libdrm-nouveau2 is already the newest version (2.4.134-1). libdrm-nouveau2 set to manually installed. libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. hostname is already the newest version (3.25). libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. libibverbs-dev is already the newest version (63.0-1). libibverbs-dev set to manually installed. binutils is already the newest version (2.46-3). binutils set to manually installed. gfortran-15 is already the newest version (15.2.0-17). gfortran-15 set to manually installed. openssh-client is already the newest version (1:10.3p1-4). openssh-client set to manually installed. libdrm2 is already the newest version (2.4.134-1). libdrm2 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libbsd0 is already the newest version (0.12.2-3). libbsd0 set to manually installed. dash is already the newest version (0.5.12-12). libpam-runtime is already the newest version (1.7.0-5). libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. time is already the newest version (1.10-0.1). time set to manually installed. autopoint is already the newest version (0.26-1). autopoint set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. libhwasan0 is already the newest version (16.1.0-1). libhwasan0 set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. mount is already the newest version (2.42.1-3). mount set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libamd-smi26 is already the newest version (7.2.0-3). libamd-smi26 set to manually installed. libatomic1 is already the newest version (16.1.0-1). libatomic1 set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libkrb5-3 is already the newest version (1.22.1-2.1). libkrb5-3 set to manually installed. gcc-15 is already the newest version (15.2.0-17). gcc-15 set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1+b1). libncursesw6 set to manually installed. librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. libhwloc-plugins is already the newest version (2.14.0-1). libhwloc-plugins set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. 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. libsystemd-shared is already the newest version (261~rc3-1). libsystemd-shared set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-17). libgfortran-15-dev set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libgcc-15-dev is already the newest version (15.2.0-17). libgcc-15-dev set to manually installed. bsdextrautils is already the newest version (2.42.1-3). bsdextrautils 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. libnl-route-3-dev is already the newest version (3.12.0-2+b1). libnl-route-3-dev set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-extra-2.1-7t64 set to manually installed. cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.1-1). libfile-stripnondeterminism-perl set to manually installed. libidn2-0 is already the newest version (2.3.8-5). libidn2-0 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b2). init-system-helpers is already the newest version (1.69). libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-10). liblocale-gettext-perl set to manually installed. libperl5.40 is already the newest version (5.40.1-8). libperl5.40 set to manually installed. libexpat1 is already the newest version (2.8.1-1). libexpat1 set to manually installed. libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. tar is already the newest version (1.35+dfsg-4). ncurses-base is already the newest version (6.6+20251231-1). file is already the newest version (1:5.47-4). file set to manually installed. debianutils is already the newest version (5.23.2). groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7+b1). libclang-common-21-dev set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). libprrte-dev is already the newest version (3.0.13-3). libprrte-dev 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. libgomp1 is already the newest version (16.1.0-1). libgomp1 set to manually installed. libacl1 is already the newest version (2.3.2-3). libjsoncpp26 is already the newest version (1.9.7-2). libjsoncpp26 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. g++-15 is already the newest version (15.2.0-17). g++-15 set to manually installed. libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. coreutils is already the newest version (9.10-1). libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libdrm-intel1 is already the newest version (2.4.134-1). libdrm-intel1 set to manually installed. libllvm21 is already the newest version (1:21.1.8-7+b1). libllvm21 set to manually installed. libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. libucx0 is already the newest version (1.20.1-1). libucx0 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.22.1-1). libngtcp2-crypto-ossl0 set to manually installed. openssl-provider-legacy is already the newest version (3.6.2-1). libdrm-dev is already the newest version (2.4.134-1). libdrm-dev set to manually installed. liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b1). libpmix2t64 set to manually installed. libsystemd0 is already the newest version (261~rc3-1). 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. libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. base-files is already the newest version (14.2). libmount1 is already the newest version (2.42.1-3). libzstd1 is already the newest version (1.5.7+dfsg-3+b2). libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. gfortran-15-x86-64-linux-gnu is already the newest version (15.2.0-17). gfortran-15-x86-64-linux-gnu set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. debconf is already the newest version (1.5.92). libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 set to manually installed. libstdc++6 is already the newest version (16.1.0-1). libstdc++6 set to manually installed. gcc-16-base is already the newest version (16.1.0-1). libblkid1 is already the newest version (2.42.1-3). libproc2-0 is already the newest version (2:4.0.4-9+b2). libproc2-0 set to manually installed. gzip is already the newest version (1.13-1). libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. libitm1 is already the newest version (16.1.0-1). libitm1 set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. chrpath is already the newest version (0.18-1). chrpath set to manually installed. The following NEW packages will be installed: pkg-config 127.0.0.1 - - [10/Jun/2026 02:54:11] "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:38515 ./ pkg-config 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (1492 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.lD3Y_t7w_E/ 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 ... 41591 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.lD3Y_t7w_E/ 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.lD3Y_t7w_E (Reading database ... 41596 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.lD3Y_t7w_E I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.lD3Y_t7w_E 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.lD3Y_t7w_E... I: success in 282.2860 seconds Downloading dependency 261 of 268: pkg-config:amd64=2.5.1-4 Downloading dependency 262 of 268: libze1:amd64=1.28.2-2 Downloading dependency 263 of 268: libitm1:amd64=16.1.0-1 Downloading dependency 264 of 268: help2man:amd64=1.49.3 Downloading dependency 265 of 268: libkeyutils1:amd64=1.6.3-6+b2 Downloading dependency 266 of 268: libcbor0.10:amd64=0.10.2-2.1+b1 Downloading dependency 267 of 268: libnl-3-dev:amd64=3.12.0-2+b1 Downloading dependency 268 of 268: chrpath:amd64=0.18-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdH4QLUQ/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1781014941 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildfLxMnr/debrebuild.sbuildrc.xvNLphhGQ7m0 sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildfLxMnr/debrebuild.tar.IMwAZFTX2bgP --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=iqtree-2.4.0+dfsg /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl41-amd64.novalocal +==============================================================================+ | iqtree 2.4.0+dfsg-2 (amd64) Wed, 10 Jun 2026 02:54:22 +0000 | +==============================================================================+ Package: iqtree Version: 2.4.0+dfsg-2 Source Version: 2.4.0+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildfLxMnr/debrebuild.tar.IMwAZFTX2bgP to /srv/rebuilderd/tmp/tmp.sbuild.SyueI4e9zQ... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Wed, 10 Jun 2026 02:54:27 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 10 Jun 2026 02:54:28 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-Px6EHz/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Wed, 10 Jun 2026 02:54:31 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64) +------------------------------------------------------------------------------+ | Build environment Wed, 10 Jun 2026 02:54:31 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.90+deb13.1-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.90-2 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-17 gcc-15_15.2.0-17 libc6-dev_2.42-16 libstdc++-15-dev_15.2.0-17 libstdc++6_16.1.0-1 linux-libc-dev_7.0.10-1 Package versions: autoconf_2.73-2 automake_1:1.18.1-4 autopoint_0.26-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42.1-3 build-essential_12.12 bzip2_1.0.8-6+b2 chrpath_0.18-1 cmake_4.3.3-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_13.32 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-x86-64-linux-gnu_15.2.0-17 gcc-16-base_16.1.0-1 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_0.26-1 gettext-base_0.26-1 gfortran-15_15.2.0-17 gfortran-15-x86-64-linux-gnu_15.2.0-17 googletest_1.17.0-1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_63.0-1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libamd-comgr3_7.0.2+dfsg-3 libamd-smi26_7.2.0-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.7-1 libasan8_16.1.0-1 libatomic1_16.1.0-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42.1-3 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-3 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-16 libc-dev-bin_2.42-16 libc-gconv-modules-extra_2.42-16 libc6_2.42-16 libc6-dev_2.42-16 libcap-ng0_0.9.3-1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-1 libclang-common-21-dev_1:21.1.8-7+b1 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl4t64_8.20.0-5 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_13.32 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-1 libdrm-common_2.4.134-1 libdrm-dev_2.4.134-1 libdrm-intel1_2.4.134-1 libdrm-nouveau2_2.4.134-1 libdrm-radeon1_2.4.134-1 libdrm2_2.4.134-1 libedit2_3.1-20260512-1 libeigen3-dev_3.4.0-5 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.1-1 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.2.0-17 libgcc-s1_16.1.0-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.2.0-17 libgfortran5_16.1.0-1 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgomp1_16.1.0-1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2.1 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-1 libhwloc-dev_2.14.0-1 libhwloc-plugins_2.14.0-1 libhwloc15_2.14.0-1 libibmad5_63.0-1 libibumad3_63.0-1 libibverbs-dev_63.0-1 libibverbs1_63.0-1 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-1 libjansson4_2.14-2+b4 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp26_1.9.7-2 libk5crypto3_1.22.1-2.1 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-2.1 libkrb5support0_1.22.1-2.1 libldap2_2.6.10+dfsg-1+b2 libllvm21_1:21.1.8-7+b1 liblocale-gettext-perl_1.07-10 liblsan0_16.1.0-1 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.1-3 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libpam-modules_1.7.0-5+b2 libpam-modules-bin_1.7.0-5+b2 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b2 libpciaccess-dev_0.17-3+b4 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3+b1 libproc2-0_2:4.0.4-9+b2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.21.5-1 libpsm2-2_11.2.185-2.1 libquadmath0_16.1.0-1 librdmacm1t64_63.0-1 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46-3 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.1-3 libsprng2_2.0a-19 libsprng2-dev_2.0a-19 libssh2-1t64_1.11.1-3 libssl3t64_3.6.2-1 libstdc++-15-dev_15.2.0-17 libstdc++6_16.1.0-1 libsystemd-shared_261~rc3-1 libsystemd0_261~rc3-1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-1 libubsan1_16.1.0-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b2 libucx0_1.20.1-1 libudev1_261~rc3-1 libunistring5_1.4.2-1 libuuid1_2.42.1-3 libuv1t64_1.52.1-4 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 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+------------------------------------------------------------------------------+ | Build Wed, 10 Jun 2026 02:54:31 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree Binary: iqtree Architecture: amd64 Version: 2.4.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Kevin Murray Homepage: http://www.iqtree.org/ Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/med-team/iqtree Vcs-Git: https://salsa.debian.org/med-team/iqtree.git Testsuite: autopkgtest Testsuite-Triggers: time Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, googletest, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree deb science optional arch=amd64 Checksums-Sha1: 56cdc0e17b6567b9d929dff852a4882ce99ac13b 2291260 iqtree_2.4.0+dfsg.orig.tar.xz 16e657ac5b3796234d4ab215c7673d73308c6c9c 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz Checksums-Sha256: cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e 2291260 iqtree_2.4.0+dfsg.orig.tar.xz b5919949246489d8ec78d070cde33d7970e785356eb8c2ec43f1d7166c919b69 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz Files: 59ee0f3268c48e3654b0113bde82d8ff 2291260 iqtree_2.4.0+dfsg.orig.tar.xz b273612f949e5447f93f2e5e7f94d0c3 22260 iqtree_2.4.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmooKPERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGerQ/+K/afBBTQUj9D0tUgWufuEgBpyB6CJ4eL LiQ80yLgL3MseEwKqnmWSN410pxiSCWwvajSPLRIg8TjpEhkfCRYlSgk9QANSo6f xAJLYIYFS5wfbbsi6mB8lo36EIqtqHrVvESU+ay3LfPeEo0mTRHr8bgDhzc0M9sB vPSHegZyTRMjSYijk7f6cgHpMSOtRfLlg+KdEjEOzyIYVTfIJE0MRj9/39N0Ke8m rwOv6JCD/7nDi/YrEJqAazXTvLKEvdrCxn4PH/dKQ39zTNaCOnyrzvxyS9zSkiG1 9KLxsFYqK4bLSKdJDzeaTbGu61vDFg/Xe/ztOrOTxyUt41NMeGUChl3eBGaLBElA GU+P+OD8ivCcChTm30Ym8HTCUYVPu3fk2HxlXNtKWjM1pssU+Z5D42tz2CZO/2QT Ece0OiV+QaxeXCJKfbe/ce0i1o6UQY6zHVxoBKvV3r0zVI1Ag928scS+1MJhwkaL F7pWR7EGMAZi2Sjva6/VrIoI9VxmXRVvDGAxSqrQrkTaogv880QLs0mwri7EyevP tXUMvlIlrQV2bRkXLcrYjKfmviSn+2KP6c2v4efGgBArT9OawWacxbESOITSnDIi E2GazXa4UD0SMnS3SIC9arxFmNvHfykttZWwANKJKIMTrue55ixCxSpnFNCUL12G YchvFXSFcv0= =DtPU -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./iqtree_2.4.0+dfsg-2.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./iqtree_2.4.0+dfsg-2.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting iqtree in /build/reproducible-path/iqtree-2.4.0+dfsg dpkg-source: info: unpacking iqtree_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.4.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-libs dpkg-source: info: applying cmake-4.patch dpkg-source: info: applying libeigen5.0.patch Check disk space ---------------- Sufficient free space for build 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=1781014941 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.4.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : omp Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:97 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") IQ-TREE flags : mpi Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib No clang-tidy (USE_CLANG_TIDY=OFF) -- Looking for unistd.h -- Looking for unistd.h - found Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (2.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY PKGCONFIG_EXECUTABLE -- Build files have been written to: /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreeavx.cpp /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelfma.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelsse.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/bitset_index.c [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashmap.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/sort.c [ 2%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree.c [ 3%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 3%] Built target pllavx [ 4%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/booster.c [ 4%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashtables_bfields.c [ 4%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/prng.c make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 5%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/stats.c [ 6%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree_utils.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 6%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 7%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsblock.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hash.c [ 10%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/lexer.c [ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancedatum.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancesblock.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/queue.c [ 16%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsemptyblock.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsexception.cpp [ 17%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/stack.c [ 18%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsreader.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 21%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 21%] Built target pll [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsstring.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstaxablock.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/mpdablock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstoken.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstreesblock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msetsblock.cpp [ 24%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 24%] Built target lsd2 make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng /usr/bin/x86_64-linux-gnu-ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/lcg64.c [ 25%] Built target ncl [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/makeseed.c make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 26%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/memory.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/store.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/primes-lcg64.c [ 27%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/checkid.c [ 28%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 28%] Built target sprng [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 28%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 28%] Built target lbfgsb make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen.c [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen_sym.c [ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/modelsblock.cpp make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 30%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/random.c [ 31%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 31%] Built target vectorclass make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/binomial_tpe.cpp [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda_sub.c [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/multinomial.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/pow_int.cpp [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest.c [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gauss.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gaussinv.cpp [ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 34%] Built target nclextra [ 34%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gausspdf.cpp [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 34%] Built target gsl make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 36%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 36%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 36%] Built target kernelsse make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/advanced.cpp [ 37%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 37%] Built target whtest [ 37%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bigint.cpp "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 38%] Built target cmaple_utils [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bipartitions.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/constraints.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/errors.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree.cpp [ 45%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 45%] Built target kernelfma make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 46%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/eigendecomposition.cpp [ 46%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 [ 46%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 46%] Built target kernelavx [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/nodes.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 46%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/circularnetwork.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/parser.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/greedy.cpp [ 48%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 48%] Built target phyloYAML [ 48%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/optimization.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/stoprule.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/tools.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/simple.cpp [ 49%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 49%] Built target decentTree [ 49%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/pllnni.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/hashsplitset.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp [ 51%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdnetwork.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/trees.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pruning.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/validation.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/checkpoint.cpp [ 54%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 54%] Built target terraphast [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/split.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitgraph.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitset.cpp [ 56%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/lpwrapper.c [ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/MPIHelper.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopd.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/graph.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtree.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtreeset.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 61%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 62%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 63%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 63%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 63%] Built target pda [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 64%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelbin.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmarkov.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldna.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactory.cpp [ 65%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 65%] Built target cmaple_model [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelprotein.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelset.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelsubst.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodel.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodelplen.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategamma.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategammainvar.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 68%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 69%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp [ 69%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 69%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterogeneity.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateinvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratekategory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefree.cpp [ 72%] Linking CXX static library libcmaple_tree.a [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefreeinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 72%] Built target cmaple_tree [ 73%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time 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'/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 73%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelcodon.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmorphology.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmixture.cpp [ 74%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 74%] Built target maple make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 75%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelunrest.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o [ 76%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomomixture.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 78%] Built target cmaple [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/pattern.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 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-I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/constrainttree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg 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-DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terrace.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a -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/iqtree-2.4.0+dfsg/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 0%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelfma.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp [ 0%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreeavx.cpp [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelsse.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/bitset_index.c [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/sort.c [ 2%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/booster.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashtables_bfields.c [ 3%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/prng.c [ 4%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/stats.c [ 5%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 5%] Built target pllavx [ 5%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree_utils.c make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 5%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 6%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ /usr/bin/x86_64-linux-gnu-ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 6%] Built target booster [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c [ 8%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsblock.cpp [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancedatum.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancesblock.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/stack.c [ 17%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsemptyblock.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsexception.cpp [ 20%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 20%] Built target pll [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsreader.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsstring.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstaxablock.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/mpdablock.cpp [ 23%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstoken.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msetsblock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstreesblock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 24%] Built target ncl make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/store.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/primes-lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 27%] Built target sprng [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/modelsblock.cpp make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 29%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 29%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 29%] Built target lsd2 make -f whtest/CMakeFiles/whtest.dir/build.make 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-DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen.c [ 29%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 29%] Built target nclextra make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 29%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 30%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 30%] Built target vectorclass [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen_sym.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/random.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda_sub.c make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/binomial_tpe.cpp [ 31%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 31%] Built target lbfgsb make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 31%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest.c [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/multinomial.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/pow_int.cpp [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gauss.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gaussinv.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gausspdf.cpp [ 34%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 34%] Built target gsl [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 36%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp [ 37%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Built target whtest make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/advanced.cpp [ 37%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Built target cmaple_utils [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bigint.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bipartitions.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 38%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 40%] Built target kernelsse make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 41%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/eigendecomposition.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp [ 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/iqtree-2.4.0+dfsg/build.serial' [ 43%] Built target kernelfma [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/constraints.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/errors.cpp [ 43%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree.cpp [ 44%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Built target phyloYAML make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda [ 44%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/circularnetwork.cpp [ 45%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/greedy.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 46%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/optimization.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/nodes.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/parser.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/stoprule.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/simple.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 48%] 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 [ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/tools.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 48%] Built target kernelavx make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 48%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp [ 50%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/hashsplitset.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/pllnni.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 51%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdnetwork.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/trees.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 52%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/validation.cpp [ 52%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/checkpoint.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 54%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 54%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 54%] Built target decentTree [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pruning.cpp [ 54%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 54%] Built target terraphast [ 54%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/split.cpp [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitgraph.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitset.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/MPIHelper.cpp [ 56%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/lpwrapper.c [ 57%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopd.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/graph.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtree.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtreeset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 63%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 63%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Built target pda [ 63%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 64%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 65%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmarkov.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelbin.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldna.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactory.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelprotein.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelset.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelsubst.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodel.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 69%] Built target cmaple_tree [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategammainvar.cpp make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 69%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterogeneity.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateinvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 71%] Built target maple [ 72%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratekategory.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefree.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefreeinvar.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachy.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachyinvar.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 74%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelcodon.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmorphology.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelunrest.cpp [ 75%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomomixture.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 78%] Built target cmaple [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignment.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/candidateset.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/constrainttree.cpp [ 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/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeplen.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd 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/build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER 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/build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terrace.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/timetree.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/treetesting.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a -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/iqtree-2.4.0+dfsg/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelfma.cpp make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreeavx.cpp [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o make[4]: Leaving 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CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylokernelsse.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/confidence_interval.cpp [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/bitset_index.c make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/io.c [ 2%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/sort.c [ 2%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/booster.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashtables_bfields.c [ 4%] Linking C static library libpllavx.a [ 4%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/prng.c cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/x86_64-linux-gnu-ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 4%] Built target pllavx [ 5%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp [ 6%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/stats.c [ 6%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree_utils.c [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Built target booster [ 6%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/estimate_root.cpp make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 6%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/lsd.cpp [ 7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hash.c [ 10%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/lexer.c [ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/models.c:47: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/readData.cpp [ 11%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/utils.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/queue.c [ 14%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsblock.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxscharactersblock.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/ssort.c [ 16%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/stack.c [ 17%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 18%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc liblsd2.a CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o CMakeFiles/lsd2.dir/src/dating.cpp.o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o CMakeFiles/lsd2.dir/src/lsd.cpp.o CMakeFiles/lsd2.dir/src/options.cpp.o CMakeFiles/lsd2.dir/src/outliers.cpp.o CMakeFiles/lsd2.dir/src/readData.cpp.o CMakeFiles/lsd2.dir/src/utils.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 18%] Built target lsd2 [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdatablock.cpp [ 18%] Linking C static library libpll.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/x86_64-linux-gnu-ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 18%] Built target pll [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 21%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/mpdablock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretematrix.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancedatum.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdistancesblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsemptyblock.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msetsblock.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/msplitsblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsexception.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsreader.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxssetreader.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/lcg64.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/makeseed.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/memory.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/store.c [ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra/modelsblock.cpp [ 26%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/primes-lcg64.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/checkid.c [ 27%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/x86_64-linux-gnu-ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 27%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 28%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb/lbfgsb_new.cpp [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsstring.cpp [ 28%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 28%] Built target nclextra [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstaxablock.cpp [ 28%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstoken.cpp /usr/bin/x86_64-linux-gnu-ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/x86_64-linux-gnu-ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Built target lbfgsb [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstreesblock.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen_sym.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/random.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 30%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda.c [ 30%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 30%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 [ 30%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/weisslambda_sub.c [ 31%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake /usr/bin/x86_64-linux-gnu-ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 31%] Built target ncl make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/x86_64-linux-gnu-ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 31%] Built target vectorclass make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/binomial_tpe.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 31%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest.c [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/multinomial.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/pow_int.cpp [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gauss.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gaussinv.cpp [ 34%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/gausspdf.cpp [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 34%] Built target gsl make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/phylo-yaml/statespace.cpp [ 35%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] Built target kernelsse [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/gzstream.cpp make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/advanced.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/logstream.cpp [ 37%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 37%] Built target whtest make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 38%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_utils.a CMakeFiles/cmaple_utils.dir/tools.cpp.o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o CMakeFiles/cmaple_utils.dir/logstream.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 38%] Built target cmaple_utils make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 40%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/eigendecomposition.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bigint.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bipartitions.cpp [ 42%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 42%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/optimization.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/bitmatrix.cpp [ 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 [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/clamped_uint.cpp /usr/bin/x86_64-linux-gnu-ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 44%] Built target kernelfma [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/constraints.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 44%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/circularnetwork.cpp [ 44%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 44%] Built target phyloYAML [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/errors.cpp [ 45%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/stoprule.cpp [ 45%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/gzstream.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree.cpp [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/multitree_iterator.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/nodes.cpp [ 47%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 47%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 47%] Built target kernelavx [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/parser.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/rooting.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/tools.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/greedy.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/simple.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/subtree_extraction.cpp [ 50%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 50%] 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/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/mutation.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/pllnni.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregion.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/supertree_helpers.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/seqregions.cpp [ 51%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/gurobiwrapper.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/trees.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/union_find.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/hashsplitset.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/checkpoint.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/validation.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/sequence.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/MPIHelper.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdnetwork.cpp [ 54%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 54%] Built target terraphast [ 54%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/alignment/alignment.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj2.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pruning.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/split.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitgraph.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/splitset.cpp [ 58%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-gcc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/lpwrapper.c [ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopd.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/graph.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtree.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/pdtreeset.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/modelbase.cpp [ 62%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_dna.cpp [ 63%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model_aa.cpp [ 63%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o CMakeFiles/utils.dir/starttree.cpp.o CMakeFiles/utils.dir/bionj.cpp.o CMakeFiles/utils.dir/bionj2.cpp.o CMakeFiles/utils.dir/progress.cpp.o CMakeFiles/utils.dir/operatingsystem.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmarkov.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelbin.cpp [ 64%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 64%] Built target pda [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldna.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactory.cpp [ 65%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 65%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 65%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/tree.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelprotein.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelset.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelsubst.cpp [ 67%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp [ 67%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 67%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodel.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodelplen.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategamma.cpp [ 69%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libcmaple_tree.a CMakeFiles/cmaple_tree.dir/tree.cpp.o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 69%] 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/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 69%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 70%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/x86_64-linux-gnu-gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/x86_64-linux-gnu-gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 70%] Built target maple [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterogeneity.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateinvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerhaeseler.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 72%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple && /usr/bin/x86_64-linux-gnu-g++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratekategory.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefree.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefreeinvar.cpp [ 73%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachy.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelcodon.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmorphology.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelunrest.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelliemarkov.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -L/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a alignment/libcmaple_alignment.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a utils/libcmaple_utils.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 76%] Built target cmaple [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomomixture.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactorymixlen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmm.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libsimulator.a CMakeFiles/simulator.dir/alisimulator.cpp.o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/substitution.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/maalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignment.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwise.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentpairwiseplen.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/superalignmentunlinked.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequence.cpp [ 83%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/sequencechunkstr.cpp [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libalignment.a CMakeFiles/alignment.dir/substitution.cpp.o CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/alignmentsummary.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o CMakeFiles/alignment.dir/sequence.cpp.o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 84%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/candidateset.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mexttree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/mtreeset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/ncbitree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/node.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genomenode.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/genometree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylonodemixlen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreepars.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreesse.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/quartet.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/supernode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/tinatree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/parstree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/discordance.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylohmm.cpp [ 94%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi 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-fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terrace.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 96%] Built target terracetphast [ 96%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libterrace.a CMakeFiles/terrace.dir/terracenode.cpp.o CMakeFiles/terrace.dir/terracetree.cpp.o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libterrace.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 96%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 97%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp [ 98%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o CMakeFiles/main.dir/alisim.cpp.o CMakeFiles/main.dir/terraceanalysis.cpp.o /usr/bin/x86_64-linux-gnu-ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [100%] Built target main make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color=" iqtree2 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2141:44: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1459:49: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1006:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1012:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/reproducible-path/iqtree-2.4.0+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.4.0+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a -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/iqtree-2.4.0+dfsg/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp ... + time /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Jun 9 2026 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy Seed: 547831 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Jun 10 03:06:24 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value Analyzing sequences: done in 8.9067e-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) 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: -11220.991 Optimal log-likelihood: -11220.877 Rate parameters: A-C: 1.44434 A-G: 2.30827 A-T: 1.70926 C-G: 1.85907 C-T: 2.80310 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: 1.492 Parameters optimization took 1 rounds (0.017 sec) Time for fast ML tree search: 0.174 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 384 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11791.072 93 23768.144 23828.434 24135.554 2 GTR+F+I 11548.425 94 23284.849 23346.648 23656.209 3 GTR+F+G4 11235.616 94 22659.231 22721.031 23030.592 4 GTR+F+I+G4 11220.874 95 22631.749 22695.082 23007.060 5 GTR+F+R2 11335.822 95 22861.644 22924.977 23236.955 6 GTR+F+R3 11220.902 97 22635.803 22702.279 23019.015 7 GTR+F+R4 11214.816 99 22627.632 22697.350 23018.746 8 GTR+F+R5 11214.688 101 22631.376 22704.440 23030.391 14 GTR+F+I+R2 11261.469 96 22714.938 22779.830 23094.200 15 GTR+F+I+R3 11217.252 98 22630.503 22698.587 23017.666 16 GTR+F+I+R4 11213.162 100 22626.325 22697.703 23021.389 26 SYM+I+G4 11224.267 92 22632.535 22691.339 22995.994 48 TVM+F+I+G4 11223.792 94 22635.584 22697.384 23006.945 70 TVMe+I+G4 11226.499 91 22634.999 22692.341 22994.507 92 TIM3+F+I+G4 11233.776 93 22653.552 22713.842 23020.962 114 TIM3e+I+G4 11237.739 90 22655.477 22711.382 23011.035 136 TIM2+F+I+G4 11237.429 93 22660.858 22721.147 23028.267 158 TIM2e+I+G4 11245.405 90 22670.810 22726.715 23026.368 180 TIM+F+I+G4 11226.597 93 22639.194 22699.484 23006.604 202 TIMe+I+G4 11233.716 90 22647.431 22703.336 23002.989 224 TPM3u+F+I+G4 11236.860 92 22657.719 22716.524 23021.179 246 TPM3+I+G4 11240.076 89 22658.152 22712.642 23009.760 268 TPM2u+F+I+G4 11240.418 92 22664.835 22723.640 23028.295 290 TPM2+I+G4 11247.561 89 22673.123 22727.613 23024.730 312 K3Pu+F+I+G4 11229.484 92 22642.967 22701.771 23006.426 334 K3P+I+G4 11235.783 89 22649.567 22704.057 23001.174 356 TN+F+I+G4 11237.682 92 22659.363 22718.167 23022.822 378 TNe+I+G4 11245.534 89 22669.068 22723.558 23020.676 400 HKY+F+I+G4 11240.690 91 22663.380 22720.723 23022.889 422 K2P+I+G4 11247.701 88 22671.402 22724.500 23019.059 444 F81+F+I+G4 11291.956 90 22763.912 22819.816 23119.470 466 JC+I+G4 11296.133 87 22766.266 22817.996 23109.972 Akaike Information Criterion: GTR+F+I+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 2.604 seconds (0h:0m:2s) Wall-clock time for ModelFinder: 2.639 seconds (0h:0m:2s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.515 / Estimate: 0.000, 0.945 / LogL: -11240.274 Init pinv, alpha: 0.012, 1.515 / Estimate: 0.083, 1.530 / LogL: -11226.498 Init pinv, alpha: 0.023, 1.515 / Estimate: 0.083, 1.527 / LogL: -11226.501 Init pinv, alpha: 0.035, 1.515 / Estimate: 0.083, 1.526 / LogL: -11226.505 Init pinv, alpha: 0.046, 1.515 / Estimate: 0.083, 1.532 / LogL: -11226.495 Init pinv, alpha: 0.058, 1.515 / Estimate: 0.083, 1.529 / LogL: -11226.500 Init pinv, alpha: 0.069, 1.515 / Estimate: 0.083, 1.534 / LogL: -11226.496 Init pinv, alpha: 0.081, 1.515 / Estimate: 0.084, 1.538 / LogL: -11226.495 Init pinv, alpha: 0.093, 1.515 / Estimate: 0.084, 1.539 / LogL: -11226.495 Init pinv, alpha: 0.104, 1.515 / Estimate: 0.084, 1.541 / LogL: -11226.496 Optimal pinv,alpha: 0.084, 1.538 / LogL: -11226.495 Parameters optimization took 1.031 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00843917 secs using 99.99% CPU Computing ML distances took 0.008569 sec (of wall-clock time) 0.008542 sec (of CPU time) Setting up auxiliary I and S matrices: done in 7.8494e-05 secs using 99.37% CPU Computing RapidNJ tree took 0.000343 sec (of wall-clock time) 0.000291 sec (of CPU time) Log-likelihood of RapidNJ tree: -11281.889 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.348 second Computing log-likelihood of 98 initial trees ... 0.420 seconds Current best score: -11226.495 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.463 Iteration 10 / LogL: -11244.733 / Time: 0h:0m:5s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 20: -11225.271 Iteration 20 / LogL: -11225.271 / Time: 0h:0m:5s Finish initializing candidate tree set (14) Current best tree score: -11225.271 / CPU time: 2.019 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 28: -11224.944 Iteration 30 / LogL: -11225.082 / Time: 0h:0m:6s (0h:0m:13s left) Estimate model parameters (epsilon = 0.100) UPDATE BEST LOG-LIKELIHOOD: -11224.925 Iteration 40 / LogL: -11227.861 / Time: 0h:0m:7s (0h:0m:11s left) Iteration 50 / LogL: -11224.965 / Time: 0h:0m:8s (0h:0m:9s left) UPDATE BEST LOG-LIKELIHOOD: -11224.916 Iteration 60 / LogL: -11228.618 / Time: 0h:0m:9s (0h:0m:7s left) Iteration 70 / LogL: -11224.978 / Time: 0h:0m:10s (0h:0m:6s left) Iteration 80 / LogL: -11225.488 / Time: 0h:0m:10s (0h:0m:5s left) Iteration 90 / LogL: -11224.964 / Time: 0h:0m:11s (0h:0m:3s left) Iteration 100 / LogL: -11224.953 / Time: 0h:0m:12s (0h:0m:2s left) Iteration 110 / LogL: -11225.565 / Time: 0h:0m:13s (0h:0m:1s left) Iteration 120 / LogL: -11225.012 / Time: 0h:0m:14s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -11224.907 TREE SEARCH COMPLETED AFTER 129 ITERATIONS / Time: 0h:0m:15s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11224.907 2. Current log-likelihood: -11224.881 Optimal log-likelihood: -11224.876 Rate parameters: A-C: 1.57840 A-G: 2.68139 A-T: 1.80097 C-G: 2.11589 C-T: 2.68139 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.561 Parameters optimization took 2 rounds (0.031 sec) BEST SCORE FOUND : -11224.876 Total tree length: 12.531 Total number of iterations: 129 CPU time used for tree search: 11.282 sec (0h:0m:11s) Wall-clock time used for tree search: 11.528 sec (0h:0m:11s) Total CPU time used: 14.984 sec (0h:0m:14s) Total wall-clock time used: 15.269 sec (0h:0m:15s) 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: Wed Jun 10 03:06:39 2026 14.98user 0.27system 0:15.27elapsed 99%CPU (0avgtext+0avgdata 17380maxresident)k 0inputs+264outputs (0major+3924minor)pagefaults 0swaps + time /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Jun 9 2026 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/iqtree2-omp -s example.phy -redo Seed: 826801 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Jun 10 03:06:39 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value Analyzing sequences: done in 8.0047e-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) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.005 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11275.951 Optimal log-likelihood: -11275.782 Rate parameters: A-C: 1.48021 A-G: 2.38709 A-T: 1.82678 C-G: 2.02541 C-T: 2.87281 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.087 Gamma shape alpha: 1.622 Parameters optimization took 1 rounds (0.016 sec) Time for fast ML tree search: 0.181 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 384 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11809.219 93 23804.439 23864.728 24171.848 2 GTR+F+I 11568.336 94 23324.672 23386.471 23696.032 3 GTR+F+G4 11293.742 94 22775.484 22837.283 23146.844 4 GTR+F+I+G4 11275.776 95 22741.552 22804.885 23116.863 5 GTR+F+R2 11395.068 95 22980.135 23043.468 23355.446 6 GTR+F+R3 11272.350 97 22738.700 22805.175 23121.912 7 GTR+F+R4 11268.002 99 22734.004 22803.722 23125.117 14 GTR+F+I+R2 11308.311 96 22808.623 22873.515 23187.884 15 GTR+F+I+R3 11269.128 98 22734.256 22802.340 23121.418 16 GTR+F+I+R4 11265.966 100 22731.933 22803.311 23126.997 26 SYM+I+G4 11279.144 92 22742.289 22801.093 23105.748 28 SYM+R3 11274.249 94 22736.499 22798.298 23107.859 29 SYM+R4 11270.947 96 22733.894 22798.786 23113.155 37 SYM+I+R3 11271.482 95 22732.964 22796.298 23108.275 48 TVM+F+I+G4 11278.301 94 22744.601 22806.401 23115.962 50 TVM+F+R3 11276.791 96 22745.581 22810.473 23124.843 51 TVM+F+R4 11271.425 98 22738.849 22806.934 23126.012 59 TVM+F+I+R3 11273.272 97 22740.544 22807.019 23123.756 70 TVMe+I+G4 11281.083 91 22744.167 22801.509 23103.675 72 TVMe+R3 11277.882 93 22741.763 22802.053 23109.173 73 TVMe+R4 11273.748 95 22737.496 22800.829 23112.807 81 TVMe+I+R3 11274.914 94 22737.828 22799.627 23109.189 92 TIM3+F+I+G4 11293.345 93 22772.690 22832.979 23140.100 94 TIM3+F+R3 11290.064 95 22770.129 22833.462 23145.440 95 TIM3+F+R4 11284.671 97 22763.342 22829.818 23146.555 103 TIM3+F+I+R3 11286.815 96 22765.630 22830.522 23144.892 114 TIM3e+I+G4 11297.353 90 22774.705 22830.610 23130.263 116 TIM3e+R3 11292.574 92 22769.149 22827.953 23132.608 117 TIM3e+R4 11288.352 94 22764.703 22826.503 23136.064 125 TIM3e+I+R3 11289.822 93 22765.644 22825.934 23133.054 136 TIM2+F+I+G4 11297.905 93 22781.809 22842.099 23149.219 138 TIM2+F+R3 11296.599 95 22783.198 22846.531 23158.509 139 TIM2+F+R4 11289.886 97 22773.772 22840.248 23156.985 147 TIM2+F+I+R3 11292.632 96 22777.265 22842.157 23156.526 158 TIM2e+I+G4 11306.178 90 22792.357 22848.261 23147.915 160 TIM2e+R3 11304.022 92 22792.044 22850.848 23155.503 161 TIM2e+R4 11298.142 94 22784.284 22846.083 23155.644 169 TIM2e+I+R3 11300.378 93 22786.755 22847.045 23154.165 180 TIM+F+I+G4 11282.316 93 22750.631 22810.921 23118.041 182 TIM+F+R3 11280.556 95 22751.112 22814.446 23126.423 183 TIM+F+R4 11274.513 97 22743.027 22809.502 23126.239 191 TIM+F+I+R3 11276.687 96 22745.374 22810.266 23124.635 202 TIMe+I+G4 11289.709 90 22759.418 22815.322 23114.976 204 TIMe+R3 11287.301 92 22758.602 22817.407 23122.061 205 TIMe+R4 11282.065 94 22752.130 22813.930 23123.491 213 TIMe+I+R3 11283.690 93 22753.379 22813.669 23120.789 224 TPM3u+F+I+G4 11295.917 92 22775.834 22834.638 23139.293 226 TPM3u+F+R3 11294.445 94 22776.891 22838.690 23148.251 227 TPM3u+F+R4 11288.200 96 22768.399 22833.291 23147.661 235 TPM3u+F+I+R3 11290.961 95 22771.923 22835.256 23147.234 246 TPM3+I+G4 11299.280 89 22776.560 22831.050 23128.167 248 TPM3+R3 11296.125 91 22774.250 22831.593 23133.759 249 TPM3+R4 11291.224 93 22768.448 22828.737 23135.857 257 TPM3+I+R3 11293.201 92 22770.402 22829.206 23133.861 268 TPM2u+F+I+G4 11300.379 92 22784.757 22843.561 23148.216 270 TPM2u+F+R3 11300.906 94 22789.811 22851.611 23161.172 271 TPM2u+F+R4 11293.294 96 22778.589 22843.481 23157.850 279 TPM2u+F+I+R3 11296.631 95 22783.261 22846.594 23158.572 290 TPM2+I+G4 11307.919 89 22793.838 22848.328 23145.445 292 TPM2+R3 11307.398 91 22796.796 22854.139 23156.305 293 TPM2+R4 11300.683 93 22787.366 22847.655 23154.776 301 TPM2+I+R3 11303.500 92 22791.000 22849.804 23154.459 312 K3Pu+F+I+G4 11284.764 92 22753.527 22812.331 23116.986 314 K3Pu+F+R3 11284.913 94 22757.825 22819.624 23129.185 315 K3Pu+F+R4 11277.792 96 22747.583 22812.475 23126.845 323 K3Pu+F+I+R3 11280.791 95 22751.582 22814.915 23126.893 334 K3P+I+G4 11291.441 89 22760.882 22815.372 23112.490 336 K3P+R3 11290.734 91 22763.469 22820.811 23122.977 337 K3P+R4 11284.512 93 22755.024 22815.314 23122.434 345 K3P+I+R3 11286.900 92 22757.799 22816.603 23121.258 356 TN+F+I+G4 11298.017 92 22780.034 22838.838 23143.493 358 TN+F+R3 11296.602 94 22781.203 22843.003 23152.564 359 TN+F+R4 11289.918 96 22771.836 22836.728 23151.098 367 TN+F+I+R3 11292.660 95 22775.319 22838.653 23150.630 378 TNe+I+G4 11306.212 89 22790.425 22844.914 23142.032 380 TNe+R3 11304.027 91 22790.054 22847.396 23149.562 381 TNe+R4 11298.203 93 22782.406 22842.696 23149.816 389 TNe+I+R3 11300.383 92 22784.767 22843.571 23148.226 400 HKY+F+I+G4 11300.500 91 22783.000 22840.342 23142.508 402 HKY+F+R3 11300.914 93 22787.828 22848.118 23155.238 403 HKY+F+R4 11293.234 95 22776.468 22839.801 23151.779 411 HKY+F+I+R3 11296.674 94 22781.348 22843.147 23152.709 422 K2P+I+G4 11307.958 88 22791.917 22845.015 23139.573 424 K2P+R3 11307.401 90 22794.803 22850.707 23150.360 425 K2P+R4 11300.671 92 22785.341 22844.145 23148.800 433 K2P+I+R3 11303.505 91 22789.011 22846.353 23148.519 444 F81+F+I+G4 11348.032 90 22876.065 22931.969 23231.623 446 F81+F+R3 11347.625 92 22879.250 22938.054 23242.709 447 F81+F+R4 11340.977 94 22869.955 22931.754 23241.315 455 F81+F+I+R3 11343.668 93 22873.336 22933.626 23240.746 466 JC+I+G4 11352.878 87 22879.757 22931.486 23223.463 468 JC+R3 11351.636 89 22881.272 22935.762 23232.879 469 JC+R4 11345.828 91 22873.657 22930.999 23233.165 477 JC+I+R3 11347.942 90 22875.884 22931.788 23231.442 Akaike Information Criterion: GTR+F+I+R4 Corrected Akaike Information Criterion: SYM+I+R3 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 6.178 seconds (0h:0m:6s) Wall-clock time for ModelFinder: 6.221 seconds (0h:0m:6s) 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, 1.636 / Estimate: 0.000, 0.971 / LogL: -11298.102 Init pinv, alpha: 0.012, 1.636 / Estimate: 0.086, 1.660 / LogL: -11281.075 Init pinv, alpha: 0.023, 1.636 / Estimate: 0.086, 1.663 / LogL: -11281.076 Init pinv, alpha: 0.035, 1.636 / Estimate: 0.086, 1.660 / LogL: -11281.082 Init pinv, alpha: 0.046, 1.636 / Estimate: 0.086, 1.658 / LogL: -11281.088 Init pinv, alpha: 0.058, 1.636 / Estimate: 0.086, 1.662 / LogL: -11281.088 Init pinv, alpha: 0.069, 1.636 / Estimate: 0.086, 1.664 / LogL: -11281.075 Init pinv, alpha: 0.081, 1.636 / Estimate: 0.086, 1.667 / LogL: -11281.076 Init pinv, alpha: 0.093, 1.636 / Estimate: 0.087, 1.669 / LogL: -11281.076 Init pinv, alpha: 0.104, 1.636 / Estimate: 0.087, 1.669 / LogL: -11281.073 Optimal pinv,alpha: 0.087, 1.669 / LogL: -11281.073 Parameters optimization took 0.999 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00850195 secs using 99.58% CPU Computing ML distances took 0.008659 sec (of wall-clock time) 0.008583 sec (of CPU time) Setting up auxiliary I and S matrices: done in 8.6709e-05 secs using 99.18% CPU Computing RapidNJ tree took 0.000370 sec (of wall-clock time) 0.000317 sec (of CPU time) Log-likelihood of RapidNJ tree: -11282.113 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.358 second Computing log-likelihood of 98 initial trees ... 0.422 seconds Current best score: -11249.684 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.135 Iteration 10 / LogL: -11226.940 / Time: 0h:0m:8s Iteration 20 / LogL: -11231.926 / Time: 0h:0m:9s Finish initializing candidate tree set (13) Current best tree score: -11225.135 / CPU time: 2.048 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11226.576 / Time: 0h:0m:10s (0h:0m:9s left) Estimate model parameters (epsilon = 0.100) UPDATE BEST LOG-LIKELIHOOD: -11224.930 Iteration 40 / LogL: -11224.930 / Time: 0h:0m:11s (0h:0m:7s left) Iteration 50 / LogL: -11226.547 / Time: 0h:0m:11s (0h:0m:5s left) Estimate model parameters (epsilon = 0.100) UPDATE BEST LOG-LIKELIHOOD: -11224.865 Iteration 60 / LogL: -11225.386 / Time: 0h:0m:12s (0h:0m:4s left) Iteration 70 / LogL: -11225.565 / Time: 0h:0m:13s (0h:0m:3s left) Iteration 80 / LogL: -11225.303 / Time: 0h:0m:14s (0h:0m:2s left) Iteration 90 / LogL: -11225.120 / Time: 0h:0m:15s (0h:0m:1s left) Iteration 100 / LogL: -11224.912 / Time: 0h:0m:16s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:16s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11224.865 Optimal log-likelihood: -11224.864 Rate parameters: A-C: 1.60606 A-G: 2.72059 A-T: 1.83129 C-G: 2.15352 C-T: 2.72059 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.560 Parameters optimization took 1 rounds (0.015 sec) BEST SCORE FOUND : -11224.864 Total tree length: 12.528 Total number of iterations: 102 CPU time used for tree search: 8.729 sec (0h:0m:8s) Wall-clock time used for tree search: 8.897 sec (0h:0m:8s) Total CPU time used: 15.959 sec (0h:0m:15s) Total wall-clock time used: 16.175 sec (0h:0m:16s) 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: Wed Jun 10 03:06:56 2026 15.96user 0.19system 0:16.18elapsed 99%CPU (0avgtext+0avgdata 17460maxresident)k 0inputs+272outputs (0major+2471minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.TXWr7I 30.95user 0.49system 0:31.50elapsed 99%CPU (0avgtext+0avgdata 17460maxresident)k 0inputs+584outputs (0major+8073minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j6 install DESTDIR=/build/reproducible-path/iqtree-2.4.0\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j6 install DESTDIR=/build/reproducible-path/iqtree-2.4.0\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.4.0+dfsg -B/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_install find debian -name iqtree2-mpi -exec chrpath --delete \{\} \; find debian -name iqtree2-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg' mkdir -p /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/share/man/man1//iqtree2.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.4.0+dfsg" /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/reproducible-path/iqtree-2.4.0+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'iqtree' in '../iqtree_2.4.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree_2.4.0+dfsg-2_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree_2.4.0+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-06-10T03:09:06Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 10 Jun 2026 03:09:07 +0000 | +------------------------------------------------------------------------------+ iqtree_2.4.0+dfsg-2_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 09 Jun 2026 16:22:21 +0200 Source: iqtree Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.4.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: iqtree - efficient phylogenetic software by maximum likelihood Closes: 1136241 Changes: iqtree (2.4.0+dfsg-2) unstable; urgency=medium . * d/watch: Use auto for Dversion-Mangle * Build using Libeigen 5.0 Closes: #1136241 * Remove redundant Priority: optional from source stanza. Checksums-Sha1: 97657341c60d02a666cd640c9a971ebb56de3551 115218848 iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb e09272681b96614d4b93b12352bcb77e78fef377 8633 iqtree_2.4.0+dfsg-2_amd64.buildinfo 06bd81fa7e91f4607e79465e9405470f2a586853 10314596 iqtree_2.4.0+dfsg-2_amd64.deb Checksums-Sha256: 7ae33622af46b2c222d3f8338123c65e0529a621187b0cf99d5802e43ad9192d 115218848 iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb 230f8d257c013f8dd1ebd1da5c6922bc6b49f4fd3569c144632b7f57e8c352d0 8633 iqtree_2.4.0+dfsg-2_amd64.buildinfo f083a47f7a44b7c9d2bfe2e999c3272ccaca80010ada9ee3dc578a7d4493d334 10314596 iqtree_2.4.0+dfsg-2_amd64.deb Files: dd390872e6aa7581db7767bd363d1132 115218848 debug optional iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb 42c224fe9837ca20a19b329bbbc48736 8633 science optional iqtree_2.4.0+dfsg-2_amd64.buildinfo 970040230f9d262e0f026159aedc690d 10314596 science optional iqtree_2.4.0+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 10 Jun 2026 03:09:08 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.4.0+dfsg-2 Checksums-Md5: dd390872e6aa7581db7767bd363d1132 115218848 iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb 970040230f9d262e0f026159aedc690d 10314596 iqtree_2.4.0+dfsg-2_amd64.deb Checksums-Sha1: 97657341c60d02a666cd640c9a971ebb56de3551 115218848 iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb 06bd81fa7e91f4607e79465e9405470f2a586853 10314596 iqtree_2.4.0+dfsg-2_amd64.deb Checksums-Sha256: 7ae33622af46b2c222d3f8338123c65e0529a621187b0cf99d5802e43ad9192d 115218848 iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb f083a47f7a44b7c9d2bfe2e999c3272ccaca80010ada9ee3dc578a7d4493d334 10314596 iqtree_2.4.0+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 10 Jun 2026 03:09:05 +0000 Build-Path: /build/reproducible-path/iqtree-2.4.0+dfsg Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 0.26-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.42.1-3), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), chrpath (= 0.18-1), cmake (= 4.3.3-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.2.0-17), cpp-15-x86-64-linux-gnu (= 15.2.0-17), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.32), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.2.0-17), g++-15-x86-64-linux-gnu (= 15.2.0-17), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.2.0-17), gcc-15-base (= 15.2.0-17), gcc-15-x86-64-linux-gnu (= 15.2.0-17), gcc-16-base (= 16.1.0-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 0.26-1), gettext-base (= 0.26-1), gfortran-15 (= 15.2.0-17), gfortran-15-x86-64-linux-gnu (= 15.2.0-17), googletest (= 1.17.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 63.0-1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libamd-comgr3 (= 7.0.2+dfsg-3), libamd-smi26 (= 7.2.0-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.7-1), libasan8 (= 16.1.0-1), libatomic1 (= 16.1.0-1), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-3), libblkid1 (= 2.42.1-3), libboost-dev (= 1.90.0.2), libboost1.90-dev (= 1.90.0-6), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-16), libc-dev-bin (= 2.42-16), libc-gconv-modules-extra (= 2.42-16), libc6 (= 2.42-16), libc6-dev (= 2.42-16), libcap-ng0 (= 0.9.3-1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-1), libclang-common-21-dev (= 1:21.1.8-7+b1), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl4t64 (= 8.20.0-5), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 13.32), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-1), libdrm-common (= 2.4.134-1), libdrm-dev (= 2.4.134-1), libdrm-intel1 (= 2.4.134-1), libdrm-nouveau2 (= 2.4.134-1), libdrm-radeon1 (= 2.4.134-1), libdrm2 (= 2.4.134-1), libedit2 (= 3.1-20260512-1), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-dev (= 2.1.12-stable-10+b2), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b2), libexpat1 (= 2.8.1-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.5.2-4), libfido2-1 (= 1.17.0-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.2-2), libgcc-15-dev (= 15.2.0-17), libgcc-s1 (= 16.1.0-1), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-15-dev (= 15.2.0-17), libgfortran5 (= 16.1.0-1), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2.1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16.1.0-1), libhwloc-dev (= 2.14.0-1), libhwloc-plugins (= 2.14.0-1), libhwloc15 (= 2.14.0-1), libibmad5 (= 63.0-1), libibumad3 (= 63.0-1), libibverbs-dev (= 63.0-1), libibverbs1 (= 63.0-1), libidn2-0 (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-1), libjansson4 (= 2.14-2+b4), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp26 (= 1.9.7-2), libk5crypto3 (= 1.22.1-2.1), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-2.1), libkrb5support0 (= 1.22.1-2.1), libldap2 (= 2.6.10+dfsg-1+b2), libllvm21 (= 1:21.1.8-7+b1), liblocale-gettext-perl (= 1.07-10), liblsan0 (= 16.1.0-1), libltdl-dev (= 2.5.4-11), libltdl7 (= 2.5.4-11), liblz4-1 (= 1.10.0-10), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.1-3), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncursesw6 (= 6.6+20251231-1+b1), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-ossl0 (= 1.22.1-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libpam-modules (= 1.7.0-5+b2), libpam-modules-bin (= 1.7.0-5+b2), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b2), libpciaccess-dev (= 0.17-3+b4), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b2), libperl5.40 (= 5.40.1-8), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 6.0.0+really5.0.9-3+b1), libproc2-0 (= 2:4.0.4-9+b2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.21.5-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16.1.0-1), librdmacm1t64 (= 63.0-1), librhash1 (= 1.4.6-1.1+b1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46-3), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.1-3), libsprng2 (= 2.0a-19), libsprng2-dev (= 2.0a-19), libssh2-1t64 (= 1.11.1-3), libssl3t64 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-17), libstdc++6 (= 16.1.0-1), libsystemd-shared (= 261~rc3-1), libsystemd0 (= 261~rc3-1), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-1), libubsan1 (= 16.1.0-1), libucc1 (= 1.7.0~rc1-1), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.20.1-1), libudev1 (= 261~rc3-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.1-3), libuv1t64 (= 1.52.1-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libxxhash0 (= 0.8.3-2+b2), libyaml-cpp-dev (= 0.8.0+dfsg-9+b1), libyaml-cpp0.8 (= 0.8.0+dfsg-9+b1), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.10-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.42.1-3), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.3p1-4), openssl-provider-legacy (= 3.6.2-1), patch (= 2.8-2), perl (= 5.40.1-8), perl-base (= 5.40.1-8), perl-modules-5.40 (= 5.40.1-8), pkg-config (= 2.5.1-4), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), procps (= 2:4.0.4-9+b2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261~rc3-1), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.10-0.1), util-linux (= 2.42.1-3), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1781014941" +------------------------------------------------------------------------------+ | Package contents Wed, 10 Jun 2026 03:09:08 +0000 | +------------------------------------------------------------------------------+ iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb ------------------------------------ new Debian package, version 2.0. size 115218848 bytes: control archive=704 bytes. 461 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: iqtree-dbgsym Source: iqtree Version: 2.4.0+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 122102 Depends: iqtree (= 2.4.0+dfsg-2) Section: debug Priority: optional Description: debug symbols for iqtree Build-Ids: 2bd4dc2e0f399d0177ce6bdbb04e0f196f2b87a9 87a5fcedf7336ce707a945e11ec597cb7df253f6 9c9be5eaff0acd8404879577ec6ec27696f41570 drwxr-xr-x root/root 0 2026-06-09 14:22 ./ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.build-id/2b/ -rw-r--r-- root/root 36221208 2026-06-09 14:22 ./usr/lib/debug/.build-id/2b/d4dc2e0f399d0177ce6bdbb04e0f196f2b87a9.debug drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.build-id/87/ -rw-r--r-- root/root 36313688 2026-06-09 14:22 ./usr/lib/debug/.build-id/87/a5fcedf7336ce707a945e11ec597cb7df253f6.debug drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.build-id/9c/ -rw-r--r-- root/root 36221448 2026-06-09 14:22 ./usr/lib/debug/.build-id/9c/9be5eaff0acd8404879577ec6ec27696f41570.debug drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 16259280 2026-06-09 14:22 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree.debug drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-06-09 14:22 ./usr/share/doc/iqtree-dbgsym -> iqtree iqtree_2.4.0+dfsg-2_amd64.deb ----------------------------- new Debian package, version 2.0. size 10314596 bytes: control archive=1548 bytes. 1436 bytes, 29 lines control 1104 bytes, 16 lines md5sums Package: iqtree Version: 2.4.0+dfsg-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 34690 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.8 (>= 0.7.0), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://www.iqtree.org/ Description: efficient phylogenetic software by maximum likelihood IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others: . * A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015) * An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013). * A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments. * Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest. * Finding best partition scheme like PartitionFinder. * Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes. * Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014) drwxr-xr-x root/root 0 2026-06-09 14:22 ./ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/bin/ -rwxr-xr-x root/root 11020920 2026-06-09 14:22 ./usr/bin/iqtree2 -rwxr-xr-x root/root 11037304 2026-06-09 14:22 ./usr/bin/iqtree2-mpi -rwxr-xr-x root/root 11020920 2026-06-09 14:22 ./usr/bin/iqtree2-omp drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/doc/iqtree/ -rw-r--r-- root/root 278 2026-06-09 14:22 ./usr/share/doc/iqtree/README.test -rw-r--r-- root/root 851 2026-06-09 14:22 ./usr/share/doc/iqtree/changelog.Debian.gz -rw-r--r-- root/root 8147 2026-06-09 14:22 ./usr/share/doc/iqtree/copyright drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/doc/iqtree/examples/ -rw-r--r-- root/root 939 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/custom_distributions.txt -rw-r--r-- root/root 2237314 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.cf -rw-r--r-- root/root 174 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.nex -rw-r--r-- root/root 34178 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/example.phy -rw-r--r-- root/root 121669 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/models.nex -rw-r--r-- root/root 47 2025-02-07 04:33 ./usr/share/doc/iqtree/examples/tree.nwk -rw-r--r-- root/root 2188 2026-06-09 14:22 ./usr/share/doc/iqtree/run-unit-test drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/man/ drwxr-xr-x root/root 0 2026-06-09 14:22 ./usr/share/man/man1/ -rw-r--r-- root/root 6993 2026-06-09 14:22 ./usr/share/man/man1/iqtree2-mpi.1.gz -rw-r--r-- root/root 6969 2026-06-09 14:22 ./usr/share/man/man1/iqtree2-omp.1.gz -rw-r--r-- root/root 6952 2026-06-09 14:22 ./usr/share/man/man1/iqtree2.1.gz +------------------------------------------------------------------------------+ | Post Build Wed, 10 Jun 2026 03:09:10 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 10 Jun 2026 03:09:10 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 10 Jun 2026 03:09:12 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3337768 Build-Time: 874 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdH4QLUQ/inputs/iqtree_2.4.0+dfsg-2.dsc Machine Architecture: amd64 Package: iqtree Package-Time: 884 Source-Version: 2.4.0+dfsg-2 Space: 3337768 Status: successful Version: 2.4.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2026-06-10T03:09:06Z Build needed 00:14:44, 3337768k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdH4QLUQ/out checking iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb: size differs for iqtree-dbgsym_2.4.0+dfsg-2_amd64.deb