=============================================================================== 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/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1_amd64.buildinfo Source: iqtree Version: 2.4.0+dfsg-1 rebuilderd-worker node: osuosl44-amd64 +------------------------------------------------------------------------------+ | Downloading sources Sun, 19 Apr 2026 07:53:24 +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 [147 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:12 https://deb.debian.org/debian-security trixie-security/main Sources [130 kB] 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 [95.0 kB] Get:15 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,984 B] Get:16 https://deb.debian.org/debian trixie-backports/main Sources [192 kB] Get:17 https://deb.debian.org/debian forky/main Sources [10.8 MB] Get:18 https://deb.debian.org/debian forky/non-free-firmware Sources [8,300 B] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.4 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.5 MB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Get:22 https://deb.debian.org/debian experimental/main Sources [436 kB] Fetched 34.5 MB in 33s (1,057 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.4.0%2bdfsg-1.dsc' iqtree_2.4.0+dfsg-1.dsc 2177 SHA256:7fdb107034c27b3ce6d8feb330521e25e26ddb50935be248ce7a6daf94e31a1b '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-1.debian.tar.xz' iqtree_2.4.0+dfsg-1.debian.tar.xz 22012 SHA256:d060b63ff91d4bbb7db33fff59c4192dc568c85f10d0867672bec734fadddeeb cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e iqtree_2.4.0+dfsg.orig.tar.xz d060b63ff91d4bbb7db33fff59c4192dc568c85f10d0867672bec734fadddeeb iqtree_2.4.0+dfsg-1.debian.tar.xz 7fdb107034c27b3ce6d8feb330521e25e26ddb50935be248ce7a6daf94e31a1b iqtree_2.4.0+dfsg-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Sun, 19 Apr 2026 07:53:57 +0000 | +------------------------------------------------------------------------------+ Rebuilding iqtree=2.4.0+dfsg-1 in /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdDDMXKo/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1_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 [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable InRelease [187 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.4 MB] Get:4 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 Packages [10.4 MB] Fetched 21.1 MB in 2s (10.2 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260410T023432Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted 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/tmp2k0kqg3c/base-passwd_3.6.8_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 (11.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwf8mc0c1/libpsm2-2_11.2.185-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Fetched 494 kB in 0s (49.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4itmv_g/autoconf_2.72-6_all.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/tmp9_f7ut7r/libffi8_3.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Fetched 480 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw4gy9mlj/libunistring5_1.4.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.68.1-1 [72.0 kB] Fetched 72.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9o7hdry1/libnghttp2-14_1.68.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.21.0-1 [25.9 kB] Fetched 25.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvrzbmd57/libngtcp2-crypto-ossl0_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (141 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiz5qlexq/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Fetched 829 kB in 0s (66.5 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpy9bgowmo/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Fetched 3654 kB in 0s (24.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp78n3ud_t/libprrte-dev_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42-3 [33.0 kB] Fetched 33.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjbg1zmt3/libuuid1_2.42-3_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/tmpxjbj6rs_/mawk_1.3.4.20260302-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.13.0-2 [23.5 kB] Fetched 23.5 kB in 0s (1097 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyu8z6hac/libhwloc-plugins_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7 [28.3 MB] Fetched 28.3 MB in 0s (183 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpga8j3uuo/libllvm21_21.1.8-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 16-20260322-1 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp2t57_k4/libgomp1_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (72.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptftzlo02/debhelper_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-1 [103 kB] Fetched 103 kB in 0s (2304 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8fim11n/libfuse3-4_3.18.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Fetched 1028 kB in 0s (6059 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1_hd9jr/libopenmpi-dev_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-14 [1790 kB] Fetched 1790 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi5aw75bd/libc6_2.42-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-16 [27.1 kB] Fetched 27.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodqlmgq3/g++-15_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b1 [716 kB] Fetched 716 kB in 0s (4969 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0f2n16d7/libfabric1_2.1.0-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5at4x7b9/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Fetched 9385 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm7halius/libamdhip64-6_6.4.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libucx0 amd64 1.20.1~rc1-2 [955 kB] Fetched 955 kB in 0s (5422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvblt2v02/libucx0_1.20.1~rc1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Fetched 298 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4jcsc9o8/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2+b1 [49.5 kB] Fetched 49.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz6ze7agb/libpipeline1_1.5.8-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzb2ljd3c/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.131-1 [39.9 kB] Fetched 39.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkbyh68sj/libdrm2_2.4.131-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 16-20260322-1 [27.0 kB] Fetched 27.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4r8s29o/libitm1_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2+b1 [132 kB] Fetched 132 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp575cje0d/libbsd0_0.12.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2+b1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplrbrj3r1/libk5crypto3_1.22.1-2+b1_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/tmp0eiorjjj/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Fetched 179 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl5lypa0t/libpam-modules_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsemanage2 amd64 3.10-1 [92.4 kB] Fetched 92.4 kB in 0s (2729 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjuf7hrdy/libsemanage2_3.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (69.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6g_qvl0_/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-14 [37.5 kB] Fetched 37.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxi37wov0/libc-dev-bin_2.42-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Fetched 883 kB in 0s (69.8 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxyejjpoe/procps_4.0.4-9+b1_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/tmpz_gyxhgh/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b1 [330 kB] Fetched 330 kB in 0s (0 B/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp4uk8r61q/libgmpxx4ldbl_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (4164 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ran6blh/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 260.1-1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp54_7jzk5/libudev1_260.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-16 [36.3 kB] Fetched 36.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ynbdfi1/gcc-15-base_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-16 [886 kB] Fetched 886 kB in 0s (67.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq8_7hdsm/libgfortran-15-dev_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 61.0-2 [44.9 kB] Fetched 44.9 kB in 0s (1450 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc3maw67u/libibmad5_61.0-2_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/tmpuh4jqs6m/libsframe3_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Fetched 795 kB in 0s (3528 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvl8c_o06/libze1_1.28.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42-3 [1221 kB] Fetched 1221 kB in 0s (90.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqecli9a/util-linux_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (61.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ym13z4w/findutils_4.10.0-3_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/tmp6ss3rxtq/intltool-debian_0.35.0+20060710.6_all.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/tmprs64rhgy/libctf-nobfd0_2.46-3_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/tmpar39acgk/libjansson4_2.14-2+b4_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/tmpi9bu2pbw/libxext6_1.3.4-1+b4_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/tmphef5kqpv/m4_1.4.21-1_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 (61.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgpxcpr9y/libmpfr6_4.2.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp_phj_l3a/g++-x86-64-linux-gnu_15.2.0-5_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/tmp43k1yl2b/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-14 [621 kB] Fetched 621 kB in 0s (57.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegczbm1a/libc-bin_2.42-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-4 [183 kB] Fetched 183 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpls8_sebp/libelf1t64_0.194-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.131-1 [9168 B] Fetched 9168 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkkzqjzc/libdrm-common_2.4.131-1_all.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 (5331 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt0cbguhz/libhsa-runtime64-1_6.4.3+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsepol2 amd64 3.10-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1i9kz7t/libsepol2_3.10-1_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 (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjnui8m96/libopenmpi40_5.0.10-1_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/tmp72aa9mt4/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0keilcl/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpif2hk750/libevent-core-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Fetched 17.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3bfvbkle/libsasl2-modules-db_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2 [62.2 kB] Fetched 62.2 kB in 0s (2002 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe17zikax/libnl-3-200_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42-3 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3av80nsx/libsmartcols1_2.42-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Fetched 98.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmphmpzfdpi/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 linux-libc-dev all 6.19.11-1 [1972 kB] Fetched 1972 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppx190kvt/linux-libc-dev_6.19.11-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Fetched 13.5 kB in 0s (318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2bmcm04/chrpath_0.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Fetched 9784 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8v6caznd/libkeyutils1_1.6.3-6+b1_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/tmpg0jw889j/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpv0_hn4h6/libxdmcp6_1.1.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Fetched 4317 kB in 0s (154 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq8rmmjgx/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b1 [41.0 kB] Fetched 41.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy2wpxk7d/bzip2_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 260.1-1 [2398 kB] Fetched 2398 kB in 0s (37.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxejudpho/libsystemd-shared_260.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Fetched 70.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk470sz0/libpam0g_1.7.0-5+b1_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/tmpzf2ys4dc/sysvinit-utils_3.18-1_amd64.deb' 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/tmp1son_wv5/libctf0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Fetched 75.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyfzktqgm/libdebhelper-perl_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdweuafpl/bash_5.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42-3 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptn3ubfg8/libmount1_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (126 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0kek43sx/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16-20260322-1 [886 kB] Fetched 886 kB in 0s (75.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqsua1n52/libgfortran5_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7 [767 kB] Fetched 767 kB in 0s (61.9 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpcpfqr_bh/libclang-common-21-dev_21.1.8-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libcap-ng0 amd64 0.9.2-1 [16.5 kB] Fetched 16.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3c5mwtsp/libcap-ng0_0.9.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-16 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr5u2mvpm/cpp-15_15.2.0-16_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/tmp_erwmgoe/dwz_0.16-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.1-1 [16.2 MB] Fetched 16.2 MB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqdlls6fk/cmake_4.3.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-16-base amd64 16-20260322-1 [35.5 kB] Fetched 35.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptxz4pbvs/gcc-16-base_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-16 [2718 kB] Fetched 2718 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy757yj7y/libgcc-15-dev_15.2.0-16_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 (1931 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz321jzeu/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1 [43.0 kB] Fetched 43.0 kB in 0s (432 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg3ce8zlm/ocl-icd-libopencl1_2.3.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libltdl7 amd64 2.5.4-10 [415 kB] Fetched 415 kB in 0s (9833 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4zepq7v0/libltdl7_2.5.4-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-3 [548 kB] Fetched 548 kB in 0s (52.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cphw3gh/libbinutils_2.46-3_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 (1036 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp55zpmd09/pkg-config_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-2 [244 kB] Fetched 244 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp132f2vj8/libssh2-1t64_1.11.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libboost-dev amd64 1.90.0.1 [3048 B] Fetched 3048 B in 0s (208 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4jrzvrw/libboost-dev_1.90.0.1_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/tmpui_ythpo/binutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 61.0-2 [64.2 kB] Fetched 64.2 kB in 0s (1692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuskd84a3/libibverbs1_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16-20260322-1 [2889 kB] Fetched 2889 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphd1bw9or/libasan8_16-20260322-1_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/tmpglk9tmjh/libbrotli1_1.2.0-3_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/tmpx8n0a7c4/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Fetched 35.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyonvq11g/pkgconf-bin_2.5.1-4_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 (64.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc1ltibxz/xz-utils_5.8.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-3 [820 kB] Fetched 820 kB in 0s (66.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp66gp28xo/libgprofng0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Fetched 68.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiwo0lxyq/libuchardet0_0.0.8-2+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 (843 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6xiifjjv/libmunge2_0.5.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Fetched 1194 kB in 0s (88.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8k4ij20/groff-base_1.23.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [24.5 kB] Fetched 24.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqe_i9gdg/libdrm-amdgpu1_2.4.131-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42-3 [99.4 kB] Fetched 99.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp36eoglbm/bsdextrautils_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp82pxl3k3/gcc-x86-64-linux-gnu_15.2.0-5_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/tmpxwzj307e/libpciaccess0_0.17-3+b4_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 (45.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd42ew76h/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Fetched 354 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx_lp2kug/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Fetched 336 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfbygbun3/libhogweed6t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Fetched 47.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphkuplum1/libpkgconf7_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16-20260322-1 [1280 kB] Fetched 1280 kB in 0s (93.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpna_92uh_/liblsan0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp-dev amd64 0.8.0+dfsg-9 [171 kB] Fetched 171 kB in 0s (8726 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_sa23cbr/libyaml-cpp-dev_0.8.0+dfsg-9_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-2 [1684 kB] Fetched 1684 kB in 0s (101 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjkxleyxg/gettext_0.23.2-2_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/tmpn4msb_vn/libpsl5t64_0.21.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libltdl-dev amd64 2.5.4-10 [168 kB] Fetched 168 kB in 0s (4887 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfbw1n57g/libltdl-dev_2.5.4-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbngnfd9f/libidn2-0_2.3.8-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libcurl4t64 amd64 8.19.0-3 [408 kB] Fetched 408 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpolgmg0vn/libcurl4t64_8.19.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2 [200 kB] Fetched 200 kB in 0s (10.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_vc4d3xh/libnl-route-3-200_3.12.0-2_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/tmpc9t86n0r/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Fetched 43.8 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7stc3862/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2+b1 [156 kB] Fetched 156 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3lpflb_c/libuv1t64_1.51.0-2+b1_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 (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpobqc1sp5/googletest_1.17.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 61.0-2 [381 kB] Fetched 381 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5ih1eor/ibverbs-providers_61.0-2_amd64.deb' Downloading dependency 1 of 273: base-passwd:amd64=3.6.8 Downloading dependency 2 of 273: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 3 of 273: autoconf:amd64=2.72-6 Downloading dependency 4 of 273: libffi8:amd64=3.5.2-4 Downloading dependency 5 of 273: libunistring5:amd64=1.4.2-1 Downloading dependency 6 of 273: libnghttp2-14:amd64=1.68.1-1 Downloading dependency 7 of 273: libngtcp2-crypto-ossl0:amd64=1.21.0-1 Downloading dependency 8 of 273: coreutils:amd64=9.10-1 Downloading dependency 9 of 273: libx11-6:amd64=2:1.8.13-1 Downloading dependency 10 of 273: libprrte-dev:amd64=3.0.13-3 Downloading dependency 11 of 273: libuuid1:amd64=2.42-3 Downloading dependency 12 of 273: mawk:amd64=1.3.4.20260302-1 Downloading dependency 13 of 273: libhwloc-plugins:amd64=2.13.0-2 Downloading dependency 14 of 273: libllvm21:amd64=1:21.1.8-7 Downloading dependency 15 of 273: libgomp1:amd64=16-20260322-1 Downloading dependency 16 of 273: debhelper:amd64=13.31 Downloading dependency 17 of 273: libfuse3-4:amd64=3.18.2-1 Downloading dependency 18 of 273: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 19 of 273: libc6:amd64=2.42-14 Downloading dependency 20 of 273: g++-15:amd64=15.2.0-16 Downloading dependency 21 of 273: libfabric1:amd64=2.1.0-1.1+b1 Downloading dependency 22 of 273: build-essential:amd64=12.12 Downloading dependency 23 of 273: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 24 of 273: libucx0:amd64=1.20.1~rc1-2 Downloading dependency 25 of 273: libpcre2-8-0:amd64=10.46-1+b1 Downloading dependency 26 of 273: libpipeline1:amd64=1.5.8-2+b1 Downloading dependency 27 of 273: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 28 of 273: libdrm2:amd64=2.4.131-1 Downloading dependency 29 of 273: libitm1:amd64=16-20260322-1 Downloading dependency 30 of 273: libbsd0:amd64=0.12.2-2+b1 Downloading dependency 31 of 273: libk5crypto3:amd64=1.22.1-2+b1 Downloading dependency 32 of 273: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 33 of 273: libpam-modules:amd64=1.7.0-5+b1 Downloading dependency 34 of 273: libsemanage2:amd64=3.10-1 Downloading dependency 35 of 273: tar:amd64=1.35+dfsg-4 Downloading dependency 36 of 273: libc-dev-bin:amd64=2.42-14 Downloading dependency 37 of 273: procps:amd64=2:4.0.4-9+b1 Downloading dependency 38 of 273: libx11-data:amd64=2:1.8.13-1 Downloading dependency 39 of 273: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 40 of 273: help2man:amd64=1.49.3 Downloading dependency 41 of 273: libudev1:amd64=260.1-1 Downloading dependency 42 of 273: gcc-15-base:amd64=15.2.0-16 Downloading dependency 43 of 273: libgfortran-15-dev:amd64=15.2.0-16 Downloading dependency 44 of 273: libibmad5:amd64=61.0-2 Downloading dependency 45 of 273: libsframe3:amd64=2.46-3 Downloading dependency 46 of 273: libze1:amd64=1.28.2-2 Downloading dependency 47 of 273: util-linux:amd64=2.42-3 Downloading dependency 48 of 273: findutils:amd64=4.10.0-3 Downloading dependency 49 of 273: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 50 of 273: libctf-nobfd0:amd64=2.46-3 Downloading dependency 51 of 273: libjansson4:amd64=2.14-2+b4 Downloading dependency 52 of 273: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 53 of 273: m4:amd64=1.4.21-1 Downloading dependency 54 of 273: libmpfr6:amd64=4.2.2-3 Downloading dependency 55 of 273: g++-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 56 of 273: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 57 of 273: libc-bin:amd64=2.42-14 Downloading dependency 58 of 273: libelf1t64:amd64=0.194-4 Downloading dependency 59 of 273: libdrm-common:amd64=2.4.131-1 Downloading dependency 60 of 273: libhsa-runtime64-1:amd64=6.4.3+dfsg-5 Downloading dependency 61 of 273: libsepol2:amd64=3.10-1 Downloading dependency 62 of 273: libopenmpi40:amd64=5.0.10-1 Downloading dependency 63 of 273: debianutils:amd64=5.23.2 Downloading dependency 64 of 273: pkgconf:amd64=2.5.1-4 Downloading dependency 65 of 273: libevent-core-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 66 of 273: libsasl2-modules-db:amd64=2.1.28+dfsg1-11 Downloading dependency 67 of 273: libnl-3-200:amd64=3.12.0-2 Downloading dependency 68 of 273: libsmartcols1:amd64=2.42-3 Downloading dependency 69 of 273: libcrypt1:amd64=1:4.5.1-1 Downloading dependency 70 of 273: linux-libc-dev:amd64=6.19.11-1 Downloading dependency 71 of 273: chrpath:amd64=0.18-1 Downloading dependency 72 of 273: libkeyutils1:amd64=1.6.3-6+b1 Downloading dependency 73 of 273: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 74 of 273: libxdmcp6:amd64=1:1.1.5-2 Downloading dependency 75 of 273: libperl5.40:amd64=5.40.1-7 Downloading dependency 76 of 273: bzip2:amd64=1.0.8-6+b1 Downloading dependency 77 of 273: libsystemd-shared:amd64=260.1-1 Downloading dependency 78 of 273: libpam0g:amd64=1.7.0-5+b1 Downloading dependency 79 of 273: sysvinit-utils:amd64=3.18-1 Downloading dependency 80 of 273: libctf0:amd64=2.46-3 Downloading dependency 81 of 273: libdebhelper-perl:amd64=13.31 Downloading dependency 82 of 273: bash:amd64=5.3-2 Downloading dependency 83 of 273: libmount1:amd64=2.42-3 Downloading dependency 84 of 273: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 85 of 273: libgfortran5:amd64=16-20260322-1 Downloading dependency 86 of 273: libclang-common-21-dev:amd64=1:21.1.8-7 Downloading dependency 87 of 273: libcap-ng0:amd64=0.9.2-1 Downloading dependency 88 of 273: cpp-15:amd64=15.2.0-16 Downloading dependency 89 of 273: dwz:amd64=0.16-4 Downloading dependency 90 of 273: cmake:amd64=4.3.1-1 Downloading dependency 91 of 273: gcc-16-base:amd64=16-20260322-1 Downloading dependency 92 of 273: libgcc-15-dev:amd64=15.2.0-16 Downloading dependency 93 of 273: openmpi-bin:amd64=5.0.10-1 Downloading dependency 94 of 273: ocl-icd-libopencl1:amd64=2.3.4-1 Downloading dependency 95 of 273: libltdl7:amd64=2.5.4-10 Downloading dependency 96 of 273: libbinutils:amd64=2.46-3 Downloading dependency 97 of 273: pkg-config:amd64=2.5.1-4 Downloading dependency 98 of 273: libssh2-1t64:amd64=1.11.1-2 Downloading dependency 99 of 273: libboost-dev:amd64=1.90.0.1 Downloading dependency 100 of 273: binutils:amd64=2.46-3 Downloading dependency 101 of 273: libibverbs1:amd64=61.0-2 Downloading dependency 102 of 273: libasan8:amd64=16-20260322-1 Downloading dependency 103 of 273: libbrotli1:amd64=1.2.0-3 Downloading dependency 104 of 273: libevent-extra-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 105 of 273: pkgconf-bin:amd64=2.5.1-4 Downloading dependency 106 of 273: xz-utils:amd64=5.8.3-1 Downloading dependency 107 of 273: libgprofng0:amd64=2.46-3 Downloading dependency 108 of 273: libuchardet0:amd64=0.0.8-2+b1 Downloading dependency 109 of 273: libmunge2:amd64=0.5.18-1 Downloading dependency 110 of 273: groff-base:amd64=1.23.0-10 Downloading dependency 111 of 273: libdrm-amdgpu1:amd64=2.4.131-1 Downloading dependency 112 of 273: bsdextrautils:amd64=2.42-3 Downloading dependency 113 of 273: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 114 of 273: libpciaccess0:amd64=0.17-3+b4 Downloading dependency 115 of 273: make:amd64=4.4.1-3 Downloading dependency 116 of 273: libtinfo6:amd64=6.6+20251231-1 Downloading dependency 117 of 273: libhogweed6t64:amd64=3.10.2-1 Downloading dependency 118 of 273: libpkgconf7:amd64=2.5.1-4 Downloading dependency 119 of 273: liblsan0:amd64=16-20260322-1 Downloading dependency 120 of 273: libyaml-cpp-dev:amd64=0.8.0+dfsg-9 Downloading dependency 121 of 273: gettext:amd64=0.23.2-2 Downloading dependency 122 of 273: libpsl5t64:amd64=0.21.5-1 Downloading dependency 123 of 273: libltdl-dev:amd64=2.5.4-10 Downloading dependency 124 of 273: libidn2-0:amd64=2.3.8-4+b1 Downloading dependency 125 of 273: libcurl4t64:amd64=8.19.0-3 Downloading dependency 126 of 273: libnl-route-3-200:amd64=3.12.0-2 Downloading dependency 127 of 273: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 128 of 273: file:amd64=1:5.46-5+b1 Downloading dependency 129 of 273: libuv1t64:amd64=1.51.0-2+b1 Downloading dependency 130 of 273: googletest:amd64=1.17.0-1 Downloading dependency 131 of 273: ibverbs-providers:amd64=61.0-2 Downloading dependency 132 of 273: libevent-openssl-2.1-7t64:amd64=2.1.12-stable-10+b2Get: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/tmp92kxp3uz/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2 [220 kB] Fetched 220 kB in 0s (1705 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkzg1bot1/libnl-route-3-dev_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2 [50.4 kB] Fetched 50.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmffhuk35/libtasn1-6_4.21.0-2_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/tmpfoes0nh7/libattr1_2.5.2-4_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/tmp3l6diz7k/libseccomp2_2.6.0-2+b1_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 (860 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm6le3qy2/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 16-20260322-1 [10.5 kB] Fetched 10.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprby2an0j/libatomic1_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaip_w6dp/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.26.2-2 [470 kB] Fetched 470 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo01mlgys/libp11-kit0_0.26.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (89.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjo0ae_6k/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0oxxiq77/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fya05yy/libncursesw6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.2+dfsg-0.1 [641 kB] Fetched 641 kB in 0s (56.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2yq_2oov/libxml2-16_2.15.2+dfsg-0.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpnpufzxfm/g++_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 260.1-1 [446 kB] Fetched 446 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpywn8o964/libsystemd0_260.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.12-3 [1520 kB] Fetched 1520 kB in 0s (102 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptq9xqxbc/libgnutls30t64_3.8.12-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16-20260322-1 [2573 kB] Fetched 2573 kB in 0s (129 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9fj4iivq/libtsan2_16-20260322-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libfido2-1 amd64 1.16.0-2+b1 [79.3 kB] Fetched 79.3 kB in 0s (640 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsf_4vutg/libfido2-1_1.16.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn86yze9b/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 login.defs all 1:4.19.3-2 [208 kB] Fetched 208 kB in 0s (4996 kB/s) dpkg-name: info: moved 'login.defs_1%3a4.19.3-2_all.deb' to '/srv/rebuilderd/tmp/tmp9oc2s7vy/login.defs_4.19.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libssl3t64 amd64 3.6.1-3 [2478 kB] Fetched 2478 kB in 0s (18.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeed2d0dm/libssl3t64_3.6.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Fetched 1034 kB in 0s (29.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ql541m_/libeigen3-dev_3.4.0-5_all.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/tmpu3ue25r3/libpam-runtime_1.7.0-5_all.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 (1273 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpicjbbli7/libxnvctrl0_535.171.04-1+b3_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 (4940 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph803dva4/libucc1_1.7.0~rc1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-16 [12.1 MB] Fetched 12.1 MB in 0s (185 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcjhupro0/cpp-15-x86-64-linux-gnu_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-14 [1992 kB] Fetched 1992 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphpn2cgix/libc6-dev_2.42-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4w3vv64/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Fetched 49.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegtu21hn/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libngtcp2-16 amd64 1.21.0-1 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0qlf_gye/libngtcp2-16_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 16-20260322-1 [765 kB] Fetched 765 kB in 0s (70.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptufaxv0k/libstdc++6_16-20260322-1_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/tmpwgrwnpv6/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 61.0-2 [30.2 kB] Fetched 30.2 kB in 0s (1315 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfsv331tr/libibumad3_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp8a25vfy1/cpp_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Fetched 445 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsdnctt2r/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-5+b1 [81.7 kB] Fetched 81.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_bwfp_gi/libjsoncpp26_1.9.6-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 61.0-2 [686 kB] Fetched 686 kB in 0s (17.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0du73oq/libibverbs-dev_61.0-2_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/tmp8sia4k54/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Fetched 451 kB in 0s (6246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp75jdam0u/libprrte3_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-16 [23.4 MB] Fetched 23.4 MB in 0s (180 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7birenwo/gcc-15-x86-64-linux-gnu_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxlffhjwm/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Fetched 19.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb_ouat09/libcom-err2_1.47.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Fetched 710 kB in 0s (62.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqxc_j7q1/libdb5.3t64_5.3.28+dfsg2-11_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 (174 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp84tyw8qr/libboost1.90-dev_1.90.0-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (104 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyi532lsz/dpkg_1.23.7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2v2xq4k/libisl23_0.27-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 16-20260322-1 [148 kB] Fetched 148 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwsml4lw1/libquadmath0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Fetched 53.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjkodkrp0/libgdbm-compat4t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16-20260322-1 [1136 kB] Fetched 1136 kB in 0s (87.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp79ym_1k8/libubsan1_16-20260322-1_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/tmpumdacpww/libmpc3_1.3.1-3_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/tmp0zhxhn9l/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20251016-1 [93.6 kB] Fetched 93.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg_qu9914/libedit2_3.1-20251016-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-2 [242 kB] Fetched 242 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxmfvijel/gettext-base_0.23.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyaml-cpp0.8 amd64 0.8.0+dfsg-9 [131 kB] Fetched 131 kB in 0s (5482 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprwpkkla_/libyaml-cpp0.8_0.8.0+dfsg-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpifybsnsq/libnettle8t64_3.10.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 perl amd64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo2ziaahs/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpmj42u7aj/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppgha744_/libmd0_1.1.0-2+b2_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/tmpvf8jmnym/libevent-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.5-1 [115 kB] Fetched 115 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphm_ydsts/libexpat1_2.7.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.13.0-2 [165 kB] Fetched 165 kB in 0s (2583 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwsf32tv3/libhwloc15_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Fetched 338 kB in 0s (30.1 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpy4ztku2v/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5 [5324 B] Fetched 5324 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpcs0wug9e/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2+b1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj4c75gtw/libgssapi-krb5-2_1.22.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 passwd amd64 1:4.19.3-2 [1284 kB] Fetched 1284 kB in 0s (15.3 MB/s) dpkg-name: info: moved 'passwd_1%3a4.19.3-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpwrrekat3/passwd_4.19.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2+b1 [31.0 kB] Fetched 31.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpescokrk5/libkrb5support0_1.22.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwc2yh8kj/hostname_3.25_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Fetched 1679 kB in 0s (95.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaubv_skc/perl-base_5.40.1-7_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/tmpz74u1p_f/liblzma5_5.8.3-1_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 (120 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw15uhpju/binutils-common_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [195 kB] Fetched 195 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxud9guy8/libldap2_2.6.10+dfsg-1+b1_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 (2340 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp07a5h1x8/libsprng2_2.0a-19_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2+b1 [336 kB] Fetched 336 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvbs6r6b2/libkrb5-3_1.22.1-2+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 (3490 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4acroz91/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b1 [28.1 kB] Fetched 28.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphyq_ys0x/libxxhash0_0.8.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Fetched 3504 B in 0s (189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0l3is8e2/mpi-default-dev_1.20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 openssh-client amd64 1:10.2p1-6 [1005 kB] Fetched 1005 kB in 0s (10.6 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.2p1-6_amd64.deb' to '/srv/rebuilderd/tmp/tmphkunc51b/openssh-client_10.2p1-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.4 [47.7 kB] Fetched 47.7 kB in 0s (2021 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_hyb8aw9/time_1.9-0.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 liblz4-1 amd64 1.10.0-8 [70.1 kB] Fetched 70.1 kB in 0s (1955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7ldtw6c/liblz4-1_1.10.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-16 [540 kB] Fetched 540 kB in 0s (51.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53zupj3w/gcc-15_15.2.0-16_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/tmp6_dhs396/libselinux1_3.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.2-3 [90.9 kB] Fetched 90.9 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp5y6ekqr5/zlib1g_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgbd52obz/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvg99fid/base-files_14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-16 [13.2 MB] Fetched 13.2 MB in 0s (166 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk3ejxigb/g++-15-x86-64-linux-gnu_15.2.0-16_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 (2589 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1yojwo5k/libprrte-bin_3.0.13-3_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 (55.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz7lyyhwo/libdpkg-perl_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 16-20260322-1 [74.0 kB] Fetched 74.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxs4ja7ye/libgcc-s1_16-20260322-1_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/tmpua2wbxml/libaudit-common_4.1.2-1_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 (61.9 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmp3ms8h72e/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Fetched 500 kB in 0s (5605 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpspk0ozvt/libsimde-dev_0.8.4~rc3-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj1x89wel/sed_4.9-2_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 (95.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp435_mxlm/dpkg-dev_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.5-1 [362 kB] Fetched 362 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuzk6ccn8/libarchive13t64_3.8.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b1 [36.7 kB] Fetched 36.7 kB in 0s (1211 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpis43lfiy/libnuma-dev_2.0.19-1+b1_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/tmpeiolpa3y/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-8 [15.2 kB] Fetched 15.2 kB in 0s (58.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg52349sz/liblocale-gettext-perl_1.07-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-16 [2779 kB] Fetched 2779 kB in 0s (117 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5vay77du/libstdc++-15-dev_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b1 [642 kB] Fetched 642 kB in 0s (15.1 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpq215dzcr/libgmp-dev_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16-20260322-1 [1580 kB] Fetched 1580 kB in 0s (94.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpezunckdh/libhwasan0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.13.0-2 [258 kB] Fetched 258 kB in 0s (9264 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpas014zp7/libhwloc-dev_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.42-3 [163 kB] Fetched 163 kB in 0s (1330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph41aumjm/mount_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcbvhpdi5/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Fetched 11.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwz44pmnp/libdebconfclient0_0.282+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/tmpikhtst7h/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b1 [22.5 kB] Fetched 22.5 kB in 0s (1499 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpscypou_f/libnuma1_2.0.19-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsemanage-common all 3.10-1 [6776 B] Fetched 6776 B in 0s (200 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjzhe5zn1/libsemanage-common_3.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Fetched 308 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplyzwbl1d/libzstd1_1.5.7+dfsg-3+b1_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 (33.2 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpoi49o2yg/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqp7rowoj/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Fetched 561 kB in 0s (54.2 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp_bq2de7e/libgmp10_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (5978 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5lyg5_gq/rpcsvc-proto_1.4.3-1_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/tmp0bdml2b1/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42-3 [172 kB] Fetched 172 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpewllnde2/libblkid1_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 61.0-2 [73.0 kB] Fetched 73.0 kB in 0s (2576 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphfxvcjie/librdmacm1t64_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 adduser all 3.155 [212 kB] Fetched 212 kB in 0s (8174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppj4uxwlj/adduser_3.155_all.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 (1967 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4y0x1so_/libsprng2-dev_2.0a-19_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/tmp5df98egq/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3 [673 kB] Fetched 673 kB in 0s (16.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5mql7uib/libpmix2t64_6.0.0+really5.0.9-3_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 (74.9 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpoqjm3joi/zlib1g-dev_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Fetched 20.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpj56bb1lo/libxau6_1.0.11-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1+b1 [8646 kB] Fetched 8646 kB in 0s (167 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7qm1qlpw/libz3-4_4.13.3-1+b1_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 1s (24.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyhcf4acv/libamd-comgr3_7.0.2+dfsg-3_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/tmp2bd8t3w6/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_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/tmpeph4lss8/libsasl2-2_2.1.28+dfsg1-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5 [5160 B] Fetched 5160 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp6zzq56_a/gcc_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1 [28.7 kB] Fetched 28.7 kB in 0s (1528 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf9qqotwv/libcbor0.10_0.10.2-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Fetched 66.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp0_si48tu/libproc2-0_4.0.4-9+b1_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 (83.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhbmka88/binutils-x86-64-linux-gnu_2.46-3_amd64.deb' Downloading dependency 133 of 273: libnl-route-3-dev:amd64=3.12.0-2 Downloading dependency 134 of 273: libtasn1-6:amd64=4.21.0-2 Downloading dependency 135 of 273: libattr1:amd64=1:2.5.2-4 Downloading dependency 136 of 273: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 137 of 273: openmpi-common:amd64=5.0.10-1 Downloading dependency 138 of 273: libatomic1:amd64=16-20260322-1 Downloading dependency 139 of 273: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 140 of 273: libp11-kit0:amd64=0.26.2-2 Downloading dependency 141 of 273: man-db:amd64=2.13.1-1 Downloading dependency 142 of 273: grep:amd64=3.12-1 Downloading dependency 143 of 273: libncursesw6:amd64=6.6+20251231-1 Downloading dependency 144 of 273: libxml2-16:amd64=2.15.2+dfsg-0.1 Downloading dependency 145 of 273: g++:amd64=4:15.2.0-5 Downloading dependency 146 of 273: libsystemd0:amd64=260.1-1 Downloading dependency 147 of 273: libgnutls30t64:amd64=3.8.12-3 Downloading dependency 148 of 273: libtsan2:amd64=16-20260322-1 Downloading dependency 149 of 273: libfido2-1:amd64=1.16.0-2+b1 Downloading dependency 150 of 273: dash:amd64=0.5.12-12 Downloading dependency 151 of 273: login.defs:amd64=1:4.19.3-2 Downloading dependency 152 of 273: libssl3t64:amd64=3.6.1-3 Downloading dependency 153 of 273: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 154 of 273: libpam-runtime:amd64=1.7.0-5 Downloading dependency 155 of 273: libxnvctrl0:amd64=535.171.04-1+b3 Downloading dependency 156 of 273: libucc1:amd64=1.7.0~rc1-1 Downloading dependency 157 of 273: cpp-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 158 of 273: libc6-dev:amd64=2.42-14 Downloading dependency 159 of 273: autotools-dev:amd64=20240727.1 Downloading dependency 160 of 273: libpam-modules-bin:amd64=1.7.0-5+b1 Downloading dependency 161 of 273: libngtcp2-16:amd64=1.21.0-1 Downloading dependency 162 of 273: libstdc++6:amd64=16-20260322-1 Downloading dependency 163 of 273: po-debconf:amd64=1.0.22 Downloading dependency 164 of 273: libibumad3:amd64=61.0-2 Downloading dependency 165 of 273: cpp:amd64=4:15.2.0-5 Downloading dependency 166 of 273: ncurses-bin:amd64=6.6+20251231-1 Downloading dependency 167 of 273: libjsoncpp26:amd64=1.9.6-5+b1 Downloading dependency 168 of 273: libibverbs-dev:amd64=61.0-2 Downloading dependency 169 of 273: debconf:amd64=1.5.92 Downloading dependency 170 of 273: libprrte3:amd64=3.0.13-3 Downloading dependency 171 of 273: gcc-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 172 of 273: libbz2-1.0:amd64=1.0.8-6+b1 Downloading dependency 173 of 273: libcom-err2:amd64=1.47.4-1 Downloading dependency 174 of 273: libdb5.3t64:amd64=5.3.28+dfsg2-11 Downloading dependency 175 of 273: libboost1.90-dev:amd64=1.90.0-6 Downloading dependency 176 of 273: dpkg:amd64=1.23.7 Downloading dependency 177 of 273: libisl23:amd64=0.27-2 Downloading dependency 178 of 273: libquadmath0:amd64=16-20260322-1 Downloading dependency 179 of 273: libgdbm-compat4t64:amd64=1.26-1+b1 Downloading dependency 180 of 273: libubsan1:amd64=16-20260322-1 Downloading dependency 181 of 273: libmpc3:amd64=1.3.1-3 Downloading dependency 182 of 273: sensible-utils:amd64=0.0.26 Downloading dependency 183 of 273: libedit2:amd64=3.1-20251016-1 Downloading dependency 184 of 273: gettext-base:amd64=0.23.2-2 Downloading dependency 185 of 273: libyaml-cpp0.8:amd64=0.8.0+dfsg-9 Downloading dependency 186 of 273: libnettle8t64:amd64=3.10.2-1 Downloading dependency 187 of 273: perl:amd64=5.40.1-7 Downloading dependency 188 of 273: libmagic1t64:amd64=1:5.46-5+b1 Downloading dependency 189 of 273: libmd0:amd64=1.1.0-2+b2 Downloading dependency 190 of 273: libevent-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 191 of 273: libexpat1:amd64=2.7.5-1 Downloading dependency 192 of 273: libhwloc15:amd64=2.13.0-2 Downloading dependency 193 of 273: libmagic-mgc:amd64=1:5.46-5+b1 Downloading dependency 194 of 273: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 195 of 273: libgssapi-krb5-2:amd64=1.22.1-2+b1 Downloading dependency 196 of 273: passwd:amd64=1:4.19.3-2 Downloading dependency 197 of 273: libkrb5support0:amd64=1.22.1-2+b1 Downloading dependency 198 of 273: hostname:amd64=3.25 Downloading dependency 199 of 273: perl-base:amd64=5.40.1-7 Downloading dependency 200 of 273: liblzma5:amd64=5.8.3-1 Downloading dependency 201 of 273: binutils-common:amd64=2.46-3 Downloading dependency 202 of 273: libldap2:amd64=2.6.10+dfsg-1+b1 Downloading dependency 203 of 273: libsprng2:amd64=2.0a-19 Downloading dependency 204 of 273: libkrb5-3:amd64=1.22.1-2+b1 Downloading dependency 205 of 273: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 206 of 273: libxxhash0:amd64=0.8.3-2+b1 Downloading dependency 207 of 273: mpi-default-dev:amd64=1.20 Downloading dependency 208 of 273: openssh-client:amd64=1:10.2p1-6 Downloading dependency 209 of 273: time:amd64=1.9-0.4 Downloading dependency 210 of 273: liblz4-1:amd64=1.10.0-8 Downloading dependency 211 of 273: gcc-15:amd64=15.2.0-16 Downloading dependency 212 of 273: libselinux1:amd64=3.10-1 Downloading dependency 213 of 273: zlib1g:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 214 of 273: gzip:amd64=1.13-1 Downloading dependency 215 of 273: base-files:amd64=14 Downloading dependency 216 of 273: g++-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 217 of 273: libprrte-bin:amd64=3.0.13-3 Downloading dependency 218 of 273: libdpkg-perl:amd64=1.23.7 Downloading dependency 219 of 273: libgcc-s1:amd64=16-20260322-1 Downloading dependency 220 of 273: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 221 of 273: automake:amd64=1:1.18.1-4 Downloading dependency 222 of 273: libsimde-dev:amd64=0.8.4~rc3-5 Downloading dependency 223 of 273: sed:amd64=4.9-2 Downloading dependency 224 of 273: dpkg-dev:amd64=1.23.7 Downloading dependency 225 of 273: libarchive13t64:amd64=3.8.5-1 Downloading dependency 226 of 273: libnuma-dev:amd64=2.0.19-1+b1 Downloading dependency 227 of 273: libacl1:amd64=2.3.2-3 Downloading dependency 228 of 273: liblocale-gettext-perl:amd64=1.07-8 Downloading dependency 229 of 273: libstdc++-15-dev:amd64=15.2.0-16 Downloading dependency 230 of 273: libgmp-dev:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 231 of 273: libhwasan0:amd64=16-20260322-1 Downloading dependency 232 of 273: libhwloc-dev:amd64=2.13.0-2 Downloading dependency 233 of 273: mount:amd64=2.42-3 Downloading dependency 234 of 273: dh-strip-nondeterminism:amd64=1.15.0-1 Downloading dependency 235 of 273: libdebconfclient0:amd64=0.282+b2 Downloading dependency 236 of 273: dh-autoreconf:amd64=22 Downloading dependency 237 of 273: libnuma1:amd64=2.0.19-1+b1 Downloading dependency 238 of 273: libsemanage-common:amd64=3.10-1 Downloading dependency 239 of 273: libzstd1:amd64=1.5.7+dfsg-3+b1 Downloading dependency 240 of 273: diffutils:amd64=1:3.12-1 Downloading dependency 241 of 273: libgdbm6t64:amd64=1.26-1+b1 Downloading dependency 242 of 273: libgmp10:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 243 of 273: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 244 of 273: init-system-helpers:amd64=1.69 Downloading dependency 245 of 273: libblkid1:amd64=2.42-3 Downloading dependency 246 of 273: librdmacm1t64:amd64=61.0-2 Downloading dependency 247 of 273: adduser:amd64=3.155 Downloading dependency 248 of 273: libsprng2-dev:amd64=2.0a-19 Downloading dependency 249 of 273: patch:amd64=2.8-2 Downloading dependency 250 of 273: libpmix2t64:amd64=6.0.0+really5.0.9-3 Downloading dependency 251 of 273: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 252 of 273: libxau6:amd64=1:1.0.11-1+b1 Downloading dependency 253 of 273: libz3-4:amd64=4.13.3-1+b1 Downloading dependency 254 of 273: libamd-comgr3:amd64=7.0.2+dfsg-3 Downloading dependency 255 of 273: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 256 of 273: libsasl2-2:amd64=2.1.28+dfsg1-11 Downloading dependency 257 of 273: gcc:amd64=4:15.2.0-5 Downloading dependency 258 of 273: libcbor0.10:amd64=0.10.2-2.1 Downloading dependency 259 of 273: libproc2-0:amd64=2:4.0.4-9+b1 Downloading dependency 260 of 273: binutils-x86-64-linux-gnu:amd64=2.46-3 Downloading dependency 261 of 273: gfortran-15-x86-64-linux-gnu:amd64=15.2.0-16Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-16 [12.8 MB] Fetched 12.8 MB in 0s (170 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5ksu5v3/gfortran-15-x86-64-linux-gnu_15.2.0-16_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 openssl-provider-legacy amd64 3.6.1-3 [314 kB] Fetched 314 kB in 0s (4865 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqadpzph4/openssl-provider-legacy_3.6.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 16-20260322-1 [45.8 kB] Fetched 45.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbzr0df3y/libcc1-0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmploa99buu/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260410T023432Z unstable/main amd64 libtool all 2.5.4-10 [539 kB] Fetched 539 kB in 0s (48.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpowsv_o_l/libtool_2.5.4-10_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 260.1-1 [3299 kB] Fetched 3299 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ywn9m74/systemd_260.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Fetched 308 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbzdv57jj/libevent-dev_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2 [105 kB] Fetched 105 kB in 0s (1563 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw3e6py40/libnl-3-dev_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-16 [19.1 kB] Fetched 19.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8dqteo2r/gfortran-15_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-2 [770 kB] Fetched 770 kB in 0s (63.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmposnn9qw8/autopoint_0.23.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Fetched 60.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp522ukq80/librtmp1_2.6-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-14 [1094 kB] Fetched 1094 kB in 0s (85.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu5a2kekq/libc-gconv-modules-extra_2.42-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1.1 [135 kB] Fetched 135 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyq3ghrfm/librhash1_1.4.6-1.1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmp8jnoof3b/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.m_NfsnLWGT as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT 127.0.0.1 - - [19/Apr/2026 07:55:47] code 404, message File not found 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:33837 ./ InRelease 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:33837 ./ Release [462 B] 127.0.0.1 - - [19/Apr/2026 07:55:47] code 404, message File not found 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:33837 ./ Release.gpg 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:33837 ./ Packages [338 kB] Fetched 339 kB in 0s (22.5 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 - - [19/Apr/2026 07:55:47] "GET /./gcc-16-base_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libc-gconv-modules-extra_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libc6_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libgcc-s1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./mawk_1.3.4.20260302-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - 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127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libbz2-1.0_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./liblzma5_5.8.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libmd0_1.1.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./tar_1.35%2bdfsg-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./dpkg_1.23.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./grep_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./ncurses-bin_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libcrypt1_4.5.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./perl-base_5.40.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libcap-ng0_0.9.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libpam0g_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libpam-modules-bin_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libpam-modules_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libblkid1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libmount1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libsmartcols1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libudev1_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libuuid1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./util-linux_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libdebconfclient0_0.282%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./libc-bin_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:55:47] "GET /./sysvinit-utils_3.18-1_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT 127.0.0.1 - - [19/Apr/2026 07:55:49] code 404, message File not found 127.0.0.1 - - [19/Apr/2026 07:55:49] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:33837 ./ InRelease 127.0.0.1 - - [19/Apr/2026 07:55:49] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:33837 ./ Release 127.0.0.1 - - [19/Apr/2026 07:55:49] code 404, message File not found 127.0.0.1 - - [19/Apr/2026 07:55:49] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:33837 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./liblocale-gettext-perl_1.07-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./mount_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libsystemd-shared_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./systemd_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libexpat1_2.7.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./login.defs_4.19.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libbsd0_0.12.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libsemanage-common_3.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libsepol2_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libsemanage2_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./passwd_4.19.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./adduser_3.155_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libstdc%2b%2b6_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libuchardet0_0.0.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./groff-base_1.23.0-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./bsdextrautils_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libgdbm6t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libpipeline1_1.5.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libseccomp2_2.6.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./man-db_2.13.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libncursesw6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libproc2-0_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./procps_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./bzip2_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libmagic-mgc_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libmagic1t64_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./file_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./gettext-base_0.23.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:03] "GET /./libedit2_3.1-20251016-1_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libdrm-amdgpu1_2.4.131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libhsa-runtime64-1_6.4.3%2bdfsg-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libamdhip64-6_6.4.3-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libibumad3_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libibmad5_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libucx0_1.20.1%7erc1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libucc1_1.7.0%7erc1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:04] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./openmpi-common_5.0.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libnl-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libnl-route-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libibverbs-dev_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libnuma-dev_2.0.19-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libltdl7_2.5.4-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libltdl-dev_2.5.4-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libhwloc-dev_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libevent-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libevent-extra-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libevent-openssl-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libevent-dev_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libprrte-bin_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libgmpxx4ldbl_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libpkgconf7_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./pkgconf-bin_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./pkgconf_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libboost1.90-dev_1.90.0-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libboost-dev_1.90.0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libyaml-cpp0.8_0.8.0%2bdfsg-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libyaml-cpp-dev_0.8.0%2bdfsg-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./googletest_1.17.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libeigen3-dev_3.4.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libsprng2_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./time_1.9-0.4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libgmp-dev_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./libsprng2-dev_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [19/Apr/2026 07:56:05] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmp8jnoof3b/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT Reading package lists... Building dependency tree... Reading state information... base-passwd is already the newest version (3.6.8). libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. autoconf is already the newest version (2.72-6). autoconf set to manually installed. libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. libnghttp2-14 is already the newest version (1.68.1-1). libnghttp2-14 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.21.0-1). libngtcp2-crypto-ossl0 set to manually installed. coreutils is already the newest version (9.10-1). libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. libuuid1 is already the newest version (2.42-3). mawk is already the newest version (1.3.4.20260302-1). libhwloc-plugins is already the newest version (2.13.0-2). libhwloc-plugins set to manually installed. libllvm21 is already the newest version (1:21.1.8-7). libllvm21 set to manually installed. libgomp1 is already the newest version (16-20260322-1). libgomp1 set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libfuse3-4 is already the newest version (3.18.2-1). libfuse3-4 set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. libc6 is already the newest version (2.42-14). g++-15 is already the newest version (15.2.0-16). g++-15 set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b1). libfabric1 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libucx0 is already the newest version (1.20.1~rc1-2). libucx0 set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b1). libpipeline1 is already the newest version (1.5.8-2+b1). libpipeline1 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. libdrm2 is already the newest version (2.4.131-1). libdrm2 set to manually installed. libitm1 is already the newest version (16-20260322-1). libitm1 set to manually installed. libbsd0 is already the newest version (0.12.2-2+b1). libbsd0 set to manually installed. libk5crypto3 is already the newest version (1.22.1-2+b1). libk5crypto3 set to manually installed. ncurses-base is already the newest version (6.6+20251231-1). libpam-modules is already the newest version (1.7.0-5+b1). libsemanage2 is already the newest version (3.10-1). libsemanage2 set to manually installed. tar is already the newest version (1.35+dfsg-4). libc-dev-bin is already the newest version (2.42-14). libc-dev-bin set to manually installed. procps is already the newest version (2:4.0.4-9+b1). procps set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b1). libgmpxx4ldbl set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. libudev1 is already the newest version (260.1-1). gcc-15-base is already the newest version (15.2.0-16). gcc-15-base set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-16). libgfortran-15-dev set to manually installed. libibmad5 is already the newest version (61.0-2). libibmad5 set to manually installed. libsframe3 is already the newest version (2.46-3). libsframe3 set to manually installed. libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. util-linux is already the newest version (2.42-3). findutils is already the newest version (4.10.0-3). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5). g++-x86-64-linux-gnu set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libc-bin is already the newest version (2.42-14). libelf1t64 is already the newest version (0.194-4). libelf1t64 set to manually installed. libdrm-common is already the newest version (2.4.131-1). libdrm-common set to manually installed. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libsepol2 is already the newest version (3.10-1). libsepol2 set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. debianutils is already the newest version (5.23.2). pkgconf is already the newest version (2.5.1-4). pkgconf 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. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libnl-3-200 is already the newest version (3.12.0-2). libnl-3-200 set to manually installed. libsmartcols1 is already the newest version (2.42-3). libcrypt1 is already the newest version (1:4.5.1-1). linux-libc-dev is already the newest version (6.19.11-1). linux-libc-dev set to manually installed. chrpath is already the newest version (0.18-1). chrpath set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b1). libkeyutils1 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2). libxdmcp6 set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. libsystemd-shared is already the newest version (260.1-1). libsystemd-shared set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). sysvinit-utils is already the newest version (3.18-1). libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. bash is already the newest version (5.3-2). libmount1 is already the newest version (2.42-3). perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. libgfortran5 is already the newest version (16-20260322-1). libgfortran5 set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7). libclang-common-21-dev set to manually installed. libcap-ng0 is already the newest version (0.9.2-1). cpp-15 is already the newest version (15.2.0-16). cpp-15 set to manually installed. dwz is already the newest version (0.16-4). dwz set to manually installed. cmake is already the newest version (4.3.1-1). cmake set to manually installed. gcc-16-base is already the newest version (16-20260322-1). libgcc-15-dev is already the newest version (15.2.0-16). libgcc-15-dev set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1). ocl-icd-libopencl1 set to manually installed. libltdl7 is already the newest version (2.5.4-10). libltdl7 set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. libssh2-1t64 is already the newest version (1.11.1-2). libssh2-1t64 set to manually installed. libboost-dev is already the newest version (1.90.0.1). libboost-dev set to manually installed. binutils is already the newest version (2.46-3). binutils set to manually installed. libibverbs1 is already the newest version (61.0-2). libibverbs1 set to manually installed. libasan8 is already the newest version (16-20260322-1). libasan8 set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 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. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.131-1). libdrm-amdgpu1 set to manually installed. bsdextrautils is already the newest version (2.42-3). bsdextrautils set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5). gcc-x86-64-linux-gnu set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1). libhogweed6t64 is already the newest version (3.10.2-1). libhogweed6t64 set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. liblsan0 is already the newest version (16-20260322-1). liblsan0 set to manually installed. libyaml-cpp-dev is already the newest version (0.8.0+dfsg-9). libyaml-cpp-dev set to manually installed. gettext is already the newest version (0.23.2-2). gettext set to manually installed. libpsl5t64 is already the newest version (0.21.5-1). libpsl5t64 set to manually installed. libltdl-dev is already the newest version (2.5.4-10). libltdl-dev set to manually installed. libidn2-0 is already the newest version (2.3.8-4+b1). libidn2-0 set to manually installed. libcurl4t64 is already the newest version (8.19.0-3). libcurl4t64 set to manually installed. libnl-route-3-200 is already the newest version (3.12.0-2). libnl-route-3-200 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). file is already the newest version (1:5.46-5+b1). file set to manually installed. libuv1t64 is already the newest version (1.51.0-2+b1). libuv1t64 set to manually installed. googletest is already the newest version (1.17.0-1). googletest set to manually installed. ibverbs-providers is already the newest version (61.0-2). ibverbs-providers 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. libnl-route-3-dev is already the newest version (3.12.0-2). libnl-route-3-dev set to manually installed. libtasn1-6 is already the newest version (4.21.0-2). libtasn1-6 set to manually installed. libattr1 is already the newest version (1:2.5.2-4). libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. libatomic1 is already the newest version (16-20260322-1). libatomic1 set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. libp11-kit0 is already the newest version (0.26.2-2). libp11-kit0 set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. grep is already the newest version (3.12-1). libncursesw6 is already the newest version (6.6+20251231-1). libncursesw6 set to manually installed. libxml2-16 is already the newest version (2.15.2+dfsg-0.1). libxml2-16 set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libsystemd0 is already the newest version (260.1-1). libgnutls30t64 is already the newest version (3.8.12-3). libgnutls30t64 set to manually installed. libtsan2 is already the newest version (16-20260322-1). libtsan2 set to manually installed. libfido2-1 is already the newest version (1.16.0-2+b1). libfido2-1 set to manually installed. dash is already the newest version (0.5.12-12). login.defs is already the newest version (1:4.19.3-2). login.defs set to manually installed. libssl3t64 is already the newest version (3.6.1-3). libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-16). cpp-15-x86-64-linux-gnu set to manually installed. libc6-dev is already the newest version (2.42-14). libc6-dev set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). libngtcp2-16 is already the newest version (1.21.0-1). libngtcp2-16 set to manually installed. libstdc++6 is already the newest version (16-20260322-1). libstdc++6 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libibumad3 is already the newest version (61.0-2). libibumad3 set to manually installed. cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1). libjsoncpp26 is already the newest version (1.9.6-5+b1). libjsoncpp26 set to manually installed. libibverbs-dev is already the newest version (61.0-2). libibverbs-dev set to manually installed. debconf is already the newest version (1.5.92). libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-16). gcc-15-x86-64-linux-gnu set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. dpkg is already the newest version (1.23.7). libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libquadmath0 is already the newest version (16-20260322-1). libquadmath0 set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. libubsan1 is already the newest version (16-20260322-1). libubsan1 set to manually installed. libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libedit2 is already the newest version (3.1-20251016-1). libedit2 set to manually installed. gettext-base is already the newest version (0.23.2-2). gettext-base set to manually installed. libyaml-cpp0.8 is already the newest version (0.8.0+dfsg-9). libyaml-cpp0.8 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1). libnettle8t64 set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. libexpat1 is already the newest version (2.7.5-1). libexpat1 set to manually installed. libhwloc15 is already the newest version (2.13.0-2). libhwloc15 set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5). cpp-x86-64-linux-gnu set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-2+b1). libgssapi-krb5-2 set to manually installed. passwd is already the newest version (1:4.19.3-2). passwd set to manually installed. libkrb5support0 is already the newest version (1.22.1-2+b1). libkrb5support0 set to manually installed. hostname is already the newest version (3.25). perl-base is already the newest version (5.40.1-7). liblzma5 is already the newest version (5.8.3-1). binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b1). libldap2 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. libkrb5-3 is already the newest version (1.22.1-2+b1). libkrb5-3 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b1). libxxhash0 set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. openssh-client is already the newest version (1:10.2p1-6). openssh-client set to manually installed. time is already the newest version (1.9-0.4). time set to manually installed. liblz4-1 is already the newest version (1.10.0-8). liblz4-1 set to manually installed. gcc-15 is already the newest version (15.2.0-16). gcc-15 set to manually installed. libselinux1 is already the newest version (3.10-1). zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). gzip is already the newest version (1.13-1). base-files is already the newest version (14). g++-15-x86-64-linux-gnu is already the newest version (15.2.0-16). g++-15-x86-64-linux-gnu set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libgcc-s1 is already the newest version (16-20260322-1). libaudit-common is already the newest version (1:4.1.2-1). automake is already the newest version (1:1.18.1-4). automake set to manually installed. libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. sed is already the newest version (4.9-2). dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. libarchive13t64 is already the newest version (3.8.5-1). libarchive13t64 set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b1). libnuma-dev set to manually installed. libacl1 is already the newest version (2.3.2-3). liblocale-gettext-perl is already the newest version (1.07-8). liblocale-gettext-perl set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-16). libstdc++-15-dev set to manually installed. libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b1). libgmp-dev set to manually installed. libhwasan0 is already the newest version (16-20260322-1). libhwasan0 set to manually installed. libhwloc-dev is already the newest version (2.13.0-2). libhwloc-dev set to manually installed. mount is already the newest version (2.42-3). mount set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libdebconfclient0 is already the newest version (0.282+b2). dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libnuma1 is already the newest version (2.0.19-1+b1). libnuma1 set to manually installed. libsemanage-common is already the newest version (3.10-1). libsemanage-common set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). diffutils is already the newest version (1:3.12-1). libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. init-system-helpers is already the newest version (1.69). libblkid1 is already the newest version (2.42-3). librdmacm1t64 is already the newest version (61.0-2). librdmacm1t64 set to manually installed. adduser is already the newest version (3.155). adduser set to manually installed. libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3). libpmix2t64 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. libxau6 is already the newest version (1:1.0.11-1+b1). libxau6 set to manually installed. libz3-4 is already the newest version (4.13.3-1+b1). libz3-4 set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 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. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. gcc is already the newest version (4:15.2.0-5). gcc set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1). libcbor0.10 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-9+b1). libproc2-0 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. gfortran-15-x86-64-linux-gnu is already the newest version (15.2.0-16). gfortran-15-x86-64-linux-gnu set to manually installed. openssl-provider-legacy is already the newest version (3.6.1-3). libcc1-0 is already the newest version (16-20260322-1). libcc1-0 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libtool is already the newest version (2.5.4-10). libtool set to manually installed. systemd is already the newest version (260.1-1). systemd set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. libnl-3-dev is already the newest version (3.12.0-2). libnl-3-dev set to manually installed. gfortran-15 is already the newest version (15.2.0-16). gfortran-15 set to manually installed. autopoint is already the newest version (0.23.2-2). autopoint set to manually installed. librtmp1 is already the newest version (2.6-1). librtmp1 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-14). librhash1 is already the newest version (1.4.6-1.1). librhash1 set to manually installed. The following NEW packages will be installed: pkg-config 127.0.0.1 - - [19/Apr/2026 07:57:02] "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:33837 ./ pkg-config 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (0 B/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT/ 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 ... 41942 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.m_NfsnLWGT/ 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.m_NfsnLWGT (Reading database ... 41947 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.m_NfsnLWGT I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.m_NfsnLWGT 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.m_NfsnLWGT... I: success in 81.4987 seconds Downloading dependency 262 of 273: openssl-provider-legacy:amd64=3.6.1-3 Downloading dependency 263 of 273: libcc1-0:amd64=16-20260322-1 Downloading dependency 264 of 273: libfile-stripnondeterminism-perl:amd64=1.15.0-1 Downloading dependency 265 of 273: libtool:amd64=2.5.4-10 Downloading dependency 266 of 273: systemd:amd64=260.1-1 Downloading dependency 267 of 273: libevent-dev:amd64=2.1.12-stable-10+b2 Downloading dependency 268 of 273: libnl-3-dev:amd64=3.12.0-2 Downloading dependency 269 of 273: gfortran-15:amd64=15.2.0-16 Downloading dependency 270 of 273: autopoint:amd64=0.23.2-2 Downloading dependency 271 of 273: librtmp1:amd64=2.6-1 Downloading dependency 272 of 273: libc-gconv-modules-extra:amd64=2.42-14 Downloading dependency 273 of 273: librhash1:amd64=1.4.6-1.1 env --chdir=/srv/rebuilderd/tmp/rebuilderdDDMXKo/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1775985538 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuild9WlPkS/debrebuild.sbuildrc.a2PyuZwWzlPp sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuild9WlPkS/debrebuild.tar.jDrGEavGln83 --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/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl44-amd64.novalocal +==============================================================================+ | iqtree 2.4.0+dfsg-1 (amd64) Sun, 19 Apr 2026 07:57:09 +0000 | +==============================================================================+ Package: iqtree Version: 2.4.0+dfsg-1 Source Version: 2.4.0+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuild9WlPkS/debrebuild.tar.jDrGEavGln83 to /srv/rebuilderd/tmp/tmp.sbuild.zsmIXBifPa... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Sun, 19 Apr 2026 07:57:14 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 19 Apr 2026 07:57:15 +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-TX0xxC/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Sun, 19 Apr 2026 07:57:18 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64) +------------------------------------------------------------------------------+ | Build environment Sun, 19 Apr 2026 07:57:18 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.74+deb13+1-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.74-2 (2026-03-08) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-16 gcc-15_15.2.0-16 libc6-dev_2.42-14 libstdc++-15-dev_15.2.0-16 libstdc++6_16-20260322-1 linux-libc-dev_6.19.11-1 Package versions: adduser_3.155 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42-3 build-essential_12.12 bzip2_1.0.8-6+b1 chrpath_0.18-1 cmake_4.3.1-1 coreutils_9.10-1 cpp_4:15.2.0-5 cpp-15_15.2.0-16 cpp-15-x86-64-linux-gnu_15.2.0-16 cpp-x86-64-linux-gnu_4:15.2.0-5 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 file_1:5.46-5+b1 findutils_4.10.0-3 g++_4:15.2.0-5 g++-15_15.2.0-16 g++-15-x86-64-linux-gnu_15.2.0-16 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-16 gcc-15-base_15.2.0-16 gcc-15-x86-64-linux-gnu_15.2.0-16 gcc-16-base_16-20260322-1 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-2 gettext-base_0.23.2-2 gfortran-15_15.2.0-16 gfortran-15-x86-64-linux-gnu_15.2.0-16 googletest_1.17.0-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_61.0-2 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.5-1 libasan8_16-20260322-1 libatomic1_16-20260322-1 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_2.42-3 libboost-dev_1.90.0.1 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b1 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-14 libc-dev-bin_2.42-14 libc-gconv-modules-extra_2.42-14 libc6_2.42-14 libc6-dev_2.42-14 libcap-ng0_0.9.2-1 libcbor0.10_0.10.2-2.1 libcc1-0_16-20260322-1 libclang-common-21-dev_1:21.1.8-7 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl4t64_8.19.0-3 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.31 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.131-1 libdrm-common_2.4.131-1 libdrm2_2.4.131-1 libedit2_3.1-20251016-1 libeigen3-dev_3.4.0-5 libelf1t64_0.194-4 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_2.7.5-1 libfabric1_2.1.0-1.1+b1 libffi8_3.5.2-4 libfido2-1_1.16.0-2+b1 libfile-stripnondeterminism-perl_1.15.0-1 libfuse3-4_3.18.2-1 libgcc-15-dev_15.2.0-16 libgcc-s1_16-20260322-1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgfortran-15-dev_15.2.0-16 libgfortran5_16-20260322-1 libgmp-dev_2:6.3.0+dfsg-5+b1 libgmp10_2:6.3.0+dfsg-5+b1 libgmpxx4ldbl_2:6.3.0+dfsg-5+b1 libgnutls30t64_3.8.12-3 libgomp1_16-20260322-1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2+b1 libhogweed6t64_3.10.2-1 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16-20260322-1 libhwloc-dev_2.13.0-2 libhwloc-plugins_2.13.0-2 libhwloc15_2.13.0-2 libibmad5_61.0-2 libibumad3_61.0-2 libibverbs-dev_61.0-2 libibverbs1_61.0-2 libidn2-0_2.3.8-4+b1 libisl23_0.27-2 libitm1_16-20260322-1 libjansson4_2.14-2+b4 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp26_1.9.6-5+b1 libk5crypto3_1.22.1-2+b1 libkeyutils1_1.6.3-6+b1 libkrb5-3_1.22.1-2+b1 libkrb5support0_1.22.1-2+b1 libldap2_2.6.10+dfsg-1+b1 libllvm21_1:21.1.8-7 liblocale-gettext-perl_1.07-8 liblsan0_16-20260322-1 libltdl-dev_2.5.4-10 libltdl7_2.5.4-10 liblz4-1_1.10.0-8 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.42-3 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1 libnghttp2-14_1.68.1-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.21.0-1 libngtcp2-crypto-ossl0_1.21.0-1 libnl-3-200_3.12.0-2 libnl-3-dev_3.12.0-2 libnl-route-3-200_3.12.0-2 libnl-route-3-dev_3.12.0-2 libnuma-dev_2.0.19-1+b1 libnuma1_2.0.19-1+b1 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2+b1 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3 libproc2-0_2:4.0.4-9+b1 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_16-20260322-1 librdmacm1t64_61.0-2 librhash1_1.4.6-1.1 librtmp1_2.6-1 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 libsemanage-common_3.10-1 libsemanage2_3.10-1 libsepol2_3.10-1 libsframe3_2.46-3 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42-3 libsprng2_2.0a-19 libsprng2-dev_2.0a-19 libssh2-1t64_1.11.1-2 libssl3t64_3.6.1-3 libstdc++-15-dev_15.2.0-16 libstdc++6_16-20260322-1 libsystemd-shared_260.1-1 libsystemd0_260.1-1 libtasn1-6_4.21.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-10 libtsan2_16-20260322-1 libubsan1_16-20260322-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b1 libucx0_1.20.1~rc1-2 libudev1_260.1-1 libunistring5_1.4.2-1 libuuid1_2.42-3 libuv1t64_1.51.0-2+b1 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b1 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.2+dfsg-0.1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b1 libyaml-cpp-dev_0.8.0+dfsg-9 libyaml-cpp0.8_0.8.0+dfsg-9 libz3-4_4.13.3-1+b1 libze1_1.28.2-2 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.19.11-1 login.defs_1:4.19.3-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42-3 mpi-default-dev_1.20 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 ocl-icd-libopencl1_2.3.4-1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.2p1-6 openssl-provider-legacy_3.6.1-3 passwd_1:4.19.3-2 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 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+b1 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 systemd_260.1-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 time_1.9-0.4 util-linux_2.42-3 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 19 Apr 2026 07:57:18 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree Binary: iqtree Architecture: amd64 Version: 2.4.0+dfsg-1 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 91570a51317be7f7558aacf1f457a663e25d6446 22012 iqtree_2.4.0+dfsg-1.debian.tar.xz Checksums-Sha256: cebc050b7717510540f49f5b824a95e64635a495864ef01163f0d6bae7e67d4e 2291260 iqtree_2.4.0+dfsg.orig.tar.xz d060b63ff91d4bbb7db33fff59c4192dc568c85f10d0867672bec734fadddeeb 22012 iqtree_2.4.0+dfsg-1.debian.tar.xz Files: 59ee0f3268c48e3654b0113bde82d8ff 2291260 iqtree_2.4.0+dfsg.orig.tar.xz 579fac9651f29c520c5dad3012d6f674 22012 iqtree_2.4.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmnbY58SHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+biRlMP/1H/Bzs1LCakwMQEEj55ir9gd2QDjuIy 1ra2QxTi1WdbgeAZXDZh6KMTz7GTWeEbag2F6s4VLCMELtlZj6EyhBRIdl8I/4Od YD66twym7JRTUitdVndMjm+LeXsJmeXs8OMcviEzN0TTOVdgWj+aW3rTesDOhrRV 2Tusd3dnhNQl3kLDUs/2wfRKcgkzy7Ovqd7bPeMoYrr7XTuq42dPDrEfDHBnjzGd zEo/qdR+wbCqQJGI8s8Fj7e19zJyVVMV1D42OOl1qVmzLl30V4HiVeVE/n1VyDqq 7HhMdy0wCZGOkR1FGwA6RNSuiKu1EnQiqhg84Yb4s8B6GQym3RxPyv7qyg1rMPKv BM9/glwd4g7QsioKMuAoExT70iEG2DYaYAhjhDmUBCc86319qnAm3p30Qeogex+P vFZoWZ0uHOh5mkVHgJtfPSzbYMQp8J7DZXznSzYys2vzvfd14NItXBKXju2A3n8D qwOl71qCTn60cpnDiE7dgOOvemfcmkveKENHvhQN20jbCTPZX2zxN+KzVVQ5NUc5 GusP+ZUEUauyeqTQYqxnmyhsFAaH/M6T5Euv3DxcKcVBfgAPr0Q+KZgtO+kAS0Xp RPfWD73xY0JeMK0+2jpGFuT01nJkLiq9QKMGo4rckSGaGndPc6l/mDctu6KfyrjJ fKCy+RKNeNEz =hxzY -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./iqtree_2.4.0+dfsg-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./iqtree_2.4.0+dfsg-1.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-1.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 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=1775985538 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-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- 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/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:94 (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 -- 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=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- 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/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:94 (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 -- 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=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- 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/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:94 (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 -- 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/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/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: 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[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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 [ 0%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o 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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cc -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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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 C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/avxLikelihood.c [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/hashmap.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/hashmap.c [ 2%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cc -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/cc -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/cc -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 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.omp/booster && /usr/bin/cc -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 [ 3%] 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/cc -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 [ 3%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/booster && /usr/bin/cc -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 [ 4%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 4%] Built target pllavx make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/stats.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/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.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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%] 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/cc -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 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%] 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/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 6%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsassumptionsblock.cpp [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 8%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 14%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/queue.c [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 20%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 21%] Built target pll [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstoken.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/readData.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 23%] 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/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 23%] Built target ncl [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/makeseed.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/sprng/memory.c [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 28%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/eigen.c [ 29%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 30%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 30%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 31%] 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/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 31%] Built target lbfgsb 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 [ 31%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 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' [ 31%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 32%] 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/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 32%] 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' [ 32%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 33%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/whtest_wrapper.cpp [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/c++ -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; | ^~~~~~~~ [ 34%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 35%] 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 [ 35%] Built target kernelsse 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 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 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 36%] 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.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 36%] 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/c++ -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 [ 36%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/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/ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 36%] Built target lsd2 [ 37%] 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/c++ -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 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' [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/utils && /usr/bin/c++ -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 [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.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 utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 "/usr/bin/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/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 [ 40%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 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' [ 41%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 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/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 43%] Built target kernelfma [ 44%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 44%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 [ 44%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.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/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 44%] Built target kernelavx [ 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.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 [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o 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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/progress.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 44%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 44%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 45%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 46%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 46%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 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' [ 46%] 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/c++ -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 [ 47%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 47%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 48%] 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/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 50%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 50%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/alignment && /usr/bin/c++ -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 [ 50%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 51%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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%] 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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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' [ 51%] Built target decentTree [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 52%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 52%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 52%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 54%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 54%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -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%] 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/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 55%] Built target terraphast [ 55%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 56%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 57%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 57%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 57%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/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/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 57%] Built target cmaple_alignment make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 58%] 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/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/model/model.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -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/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -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/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 63%] Built target pda [ 63%] 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/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/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 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.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/c++ -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 [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o [ 64%] 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/c++ -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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/c++ -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 [ 64%] 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/c++ -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 [ 64%] 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/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/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 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.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/modelbin.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelbin.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactory.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 69%] Built target cmaple_tree [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 70%] 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/c++ -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 [ 71%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 [ 72%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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%] 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/gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 72%] Built target maple [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 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' [ 74%] 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/c++ -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 [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmorphology.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmixture.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1975:38, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘calSiteLhs_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1964:8, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2051:47, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2141:44: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1295:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1284:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1370:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1459:49: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:744:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:708:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1006:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:811:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:887:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:264:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:843:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1012:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1248:29: note: destination object of size 32 allocated by ‘operator new’ [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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' [ 77%] Built target cmaple [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/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/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/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/ranlib libsimulator.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp' [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/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/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/iqtree.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemix.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtreemixhmm.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/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/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 [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terracetphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/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/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/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' [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/c++ -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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/c++ -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 [ 97%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 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/c++ -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/c++ -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/c++ -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/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.omp/main && /usr/bin/c++ -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/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/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/c++ -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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -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 -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' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[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 booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build 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 [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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 C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.serial/booster && /usr/bin/cc -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/cc -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/cc -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/cc -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/cc -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/cc -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/cc -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/cc -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/cc -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/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/booster/tree_utils.c [ 6%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/dating.cpp [ 6%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 6%] Built target booster make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.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' [ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 10%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ /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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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)); | ^~~~~~~~~~~~~~~~~~ [ 11%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ 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' [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 14%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 16%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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) * | ^~~~~~~~~~~~~~~~~~ [ 18%] 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/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 18%] Built target pll make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 20%] 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/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/ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 20%] 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.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' [ 21%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 21%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 21%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 22%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 22%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 22%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 23%] 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/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 23%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 24%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 24%] 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/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 24%] 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.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 24%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 25%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 26%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 27%] 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 27%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 30%] 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/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 30%] Built target whtest 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' [ 30%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/vectorclass/instrset_detect.cpp [ 31%] 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/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 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.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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 [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 32%] Built target nclextra [ 32%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/gsl/pow_int.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/utils && /usr/bin/c++ -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 [ 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/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+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/c++ -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 /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; | ^~~~~~~~ [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -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 [ 35%] 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/c++ -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 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 36%] 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/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/gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 36%] Built target cmaple_utils make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.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' [ 36%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 37%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 37%] Built target kernelsse 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' [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/decenttree.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 40%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/starttree.cpp [ 41%] 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/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 41%] 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 [ 41%] 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.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 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 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' [ 42%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 42%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 42%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 42%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 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/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Built target phyloYAML 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' [ 44%] 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/c++ -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 [ 44%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 44%] Built target kernelavx [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 44%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 45%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 46%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 46%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 47%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -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 [ 47%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 48%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/operatingsystem.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 49%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 49%] 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/c++ -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 [ 50%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/simple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 50%] 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/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 52%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 53%] 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/c++ -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 [ 53%] 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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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' [ 53%] Built target decentTree [ 53%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 53%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/trees.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 53%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 54%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 55%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 55%] 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/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/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 55%] Built target cmaple_alignment [ 56%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 56%] 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/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 56%] Built target terraphast [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 57%] 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/c++ -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 [ 57%] 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/c++ -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 [ 57%] 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/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 58%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] 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/c++ -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 [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 62%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/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/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -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/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/updatingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -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/c++ -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 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/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 64%] Built target pda [ 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/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/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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 [ 67%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 67%] Built target cmaple_tree [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelprotein.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelset.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 68%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodel.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategamma.cpp [ 69%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 69%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgamma.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 71%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/main/main.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratecontinuousgammainvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefree.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.serial/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.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachy.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateheterotachyinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelunrest.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:271:21, inlined from ‘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’ [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomomixture.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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' [ 76%] Built target cmaple [ 77%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmgm.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelhmmtm.cpp [ 78%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/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/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/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 [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 80%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/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/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/alignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/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/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 [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/matree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylosupertreeunlinked.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/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/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 terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build 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]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial' [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terracetphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 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.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracenode.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/presenceabsencematrix.cpp [ 96%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/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/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/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' [ 97%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 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.serial/main && /usr/bin/c++ -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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/c++ -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 [ 98%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/c++ -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 [ 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/c++ -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/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/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/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/terraceanalysis.cpp [100%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/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/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/c++ -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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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/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/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 -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: 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]: 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 booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build 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 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' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 0%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/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.mpi/booster && /usr/bin/cc -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]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -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/cc -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/cc -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/cc -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/cc -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 [ 4%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 4%] Built target pllavx [ 4%] 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/cc -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 5%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/booster && /usr/bin/cc -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 [ 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/cc -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/cc -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/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Built target booster make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 7%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 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 [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o [ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 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' [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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)); | ^~~~~~~~~~~~~~~~~~ /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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.4.0+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 12%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/lsd2/src/outliers.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 12%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsdiscretedatum.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree-2.4.0+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 18%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 20%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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); | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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) * | ^~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 21%] 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/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 21%] Built target pll [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxsreader.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxssetreader.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/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/ranlib liblsd2.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 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.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' [ 25%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 25%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 25%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 26%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 27%] Built target sprng [ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 27%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 27%] Built target ncl 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 29%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 29%] Built target lbfgsb 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' [ 29%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/whtest/random.c [ 31%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 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.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' [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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_sub.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 32%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o [ 33%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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 /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 33%] Built target nclextra [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 33%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/gaussinv.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 34%] 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/c++ -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 [ 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/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 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.mpi/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/operatingsystem.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 35%] 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.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%] 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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 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/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 36%] Built target whtest [ 37%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 38%] 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/c++ -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 [ 38%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/utils && /usr/bin/c++ -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 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' [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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%] 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 [ 40%] 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/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/gcc-ranlib-15" libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 40%] Built target cmaple_utils [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 40%] Built target kernelavx [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 41%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 42%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 43%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 44%] 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/errors.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 44%] 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.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' [ 45%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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%] 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 [ 46%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 46%] 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.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' [ 46%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 46%] 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/c++ -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 [ 47%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/c++ -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 [ 48%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/alignment && /usr/bin/c++ -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 [ 49%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 49%] 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/c++ -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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 50%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 [ 51%] 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/c++ -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 [ 52%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 52%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 52%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 53%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/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 [ 54%] 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/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/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 54%] Built target cmaple_alignment [ 55%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 55%] 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 [ 55%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 55%] Built target terraphast [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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' [ 57%] 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/c++ -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 [ 57%] 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/c++ -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 [ 57%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 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/c++ -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 [ 58%] 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/c++ -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 [ 60%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/utils/bionj.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/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 [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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%] 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/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/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 61%] Built target cmaple_model [ 62%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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 pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/c++ -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 [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/c++ -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 [ 64%] 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/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/traversingnode.cpp [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/tree/phylonode.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/pda/ecopdmtreeset.cpp [ 64%] Linking CXX static library 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/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 64%] Built target pda [ 64%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/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/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 65%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldna.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelbin.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modeldnaerror.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelfactory.cpp [ 67%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/gcc-ranlib-15" libcmaple_tree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 67%] Built target cmaple_tree [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 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' [ 67%] 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/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/system -I/usr/share/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelset.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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%] 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/gcc-ar-15" qc libmaple.a CMakeFiles/maple.dir/cmaple.cpp.o "/usr/bin/gcc-ranlib-15" libmaple.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 68%] Built target maple [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/partitionmodelplen.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rategamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 71%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple && /usr/bin/c++ -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 [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/rateinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerdiscrete.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratekategory.cpp [ 73%] Linking CXX executable cmaple [ 73%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o 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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/ratefreeinvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelmorphology.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/model/modelpomo.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 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’ [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 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’ [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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' [ 78%] Built target cmaple [ 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/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/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 78%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 78%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 80%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/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/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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/pattern.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/pattern.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_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/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/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 [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/tree/iqtree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_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/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/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 94%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.4.0+dfsg /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi' [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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 [ 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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-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%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/terracetphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.4.0+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/terracetphast/terracetphast.cpp [ 96%] 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/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/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/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/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/phylotesting.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/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/c++ -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 cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/c++ -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 [ 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/c++ -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 [ 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/c++ -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 [ 98%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.4.0+dfsg -I/build/reproducible-path/iqtree-2.4.0+dfsg/after -I/build/reproducible-path/iqtree-2.4.0+dfsg/system -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:133:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 133 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:1268:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1268 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phylotesting.cpp:43: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree-2.4.0+dfsg/main/phyloanalysis.cpp:31: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree-2.4.0+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree-2.4.0+dfsg/build.mpi/main && /usr/bin/c++ -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/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/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/c++ -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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 Apr 12 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: 619024 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sun Apr 19 08:08:47 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 17 sequences with 1998 columns, 1152 distinct patterns 1009 parsimony-informative, 303 singleton sites, 686 constant sites Gap/Ambiguity Composition p-value Analyzing sequences: done in 4.3971e-05 secs 1 LngfishAu 0.15% passed 6.20% 2 LngfishSA 0.00% failed 0.62% 3 LngfishAf 0.05% failed 1.60% 4 Frog 0.05% passed 58.01% 5 Turtle 0.15% passed 44.25% 6 Sphenodon 0.10% passed 59.78% 7 Lizard 0.90% passed 38.67% 8 Crocodile 0.35% failed 2.51% 9 Bird 0.00% failed 0.00% 10 Human 0.00% failed 0.85% 11 Seal 0.00% passed 68.93% 12 Cow 0.00% passed 59.11% 13 Whale 0.00% passed 97.83% 14 Mouse 0.05% failed 1.43% 15 Rat 0.00% passed 39.69% 16 Platypus 0.00% failed 3.46% 17 Opossum 0.00% failed 0.01% **** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 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: -21149.239 Optimal log-likelihood: -21149.100 Rate parameters: A-C: 3.73650 A-G: 5.18609 A-T: 3.83480 C-G: 0.41900 C-T: 15.29543 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 Gamma shape alpha: 0.739 Parameters optimization took 1 rounds (0.030 sec) Time for fast ML tree search: 0.310 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 1998 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 22701.500 39 45481.000 45482.593 45699.396 2 GTR+F+I 21615.547 40 43311.094 43312.770 43535.090 3 GTR+F+G4 21155.970 40 42391.940 42393.616 42615.936 4 GTR+F+I+G4 21148.849 41 42379.699 42381.459 42609.295 5 GTR+F+R2 21235.660 41 42553.320 42555.081 42782.916 6 GTR+F+R3 21147.079 43 42380.157 42382.094 42620.953 7 GTR+F+R4 21146.626 45 42383.252 42385.373 42635.247 14 GTR+F+I+R2 21174.433 42 42432.866 42434.714 42668.062 15 GTR+F+I+R3 21146.997 44 42381.994 42384.022 42628.390 16 GTR+F+I+R4 21146.784 46 42385.568 42387.785 42643.164 25 SYM+G4 21317.766 37 42709.531 42710.966 42916.728 26 SYM+I+G4 21306.372 38 42688.744 42690.257 42901.540 47 TVM+F+G4 21300.229 39 42678.458 42680.051 42896.854 48 TVM+F+I+G4 21288.393 40 42656.786 42658.462 42880.782 69 TVMe+G4 21422.115 36 42916.230 42917.589 43117.827 70 TVMe+I+G4 21407.658 37 42889.317 42890.751 43096.513 91 TIM3+F+G4 21367.928 38 42811.857 42813.370 43024.653 92 TIM3+F+I+G4 21359.551 39 42797.102 42798.696 43015.498 113 TIM3e+G4 21717.449 35 43504.899 43506.183 43700.895 114 TIM3e+I+G4 21708.477 36 43488.954 43490.313 43690.551 135 TIM2+F+G4 21159.731 38 42395.462 42396.975 42608.259 136 TIM2+F+I+G4 21152.613 39 42383.226 42384.820 42601.623 157 TIM2e+G4 21320.879 35 42711.758 42713.042 42907.754 158 TIM2e+I+G4 21309.057 36 42690.113 42691.472 42891.710 179 TIM+F+G4 21368.784 38 42813.567 42815.080 43026.364 180 TIM+F+I+G4 21360.272 39 42798.545 42800.138 43016.941 201 TIMe+G4 21718.123 35 43506.246 43507.531 43702.243 202 TIMe+I+G4 21709.148 36 43490.297 43491.655 43691.893 223 TPM3u+F+G4 21488.913 37 43051.825 43053.260 43259.022 224 TPM3u+F+I+G4 21474.794 38 43025.588 43027.101 43238.385 245 TPM3+G4 21847.238 34 43762.476 43763.689 43952.873 246 TPM3+I+G4 21833.461 35 43736.923 43738.207 43932.919 267 TPM2u+F+G4 21303.761 37 42681.522 42682.956 42888.718 268 TPM2u+F+I+G4 21291.570 38 42659.139 42660.652 42871.936 289 TPM2+G4 21424.804 34 42917.607 42918.820 43108.004 290 TPM2+I+G4 21410.107 35 42890.214 42891.498 43086.210 311 K3Pu+F+G4 21489.344 37 43052.688 43054.122 43259.884 312 K3Pu+F+I+G4 21475.259 38 43026.519 43028.032 43239.315 333 K3P+G4 21847.491 34 43762.981 43764.194 43953.378 334 K3P+I+G4 21833.614 35 43737.229 43738.513 43933.225 355 TN+F+G4 21369.057 37 42812.114 42813.549 43019.310 356 TN+F+I+G4 21360.716 38 42797.432 42798.945 43010.228 377 TNe+G4 21718.193 34 43504.387 43505.599 43694.783 378 TNe+I+G4 21709.196 35 43488.392 43489.677 43684.389 399 HKY+F+G4 21489.748 36 43051.496 43052.854 43253.092 400 HKY+F+I+G4 21475.591 37 43025.182 43026.617 43232.378 421 K2P+G4 21847.674 33 43761.348 43762.491 43946.145 422 K2P+I+G4 21833.840 34 43735.679 43736.892 43926.076 443 F81+F+G4 22031.579 35 44133.158 44134.443 44329.155 444 F81+F+I+G4 22019.146 36 44110.291 44111.650 44311.888 465 JC+G4 22258.086 32 44580.171 44581.246 44759.368 466 JC+I+G4 22245.386 33 44556.771 44557.914 44741.568 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 5.358 seconds (0h:0m:5s) Wall-clock time for ModelFinder: 5.399 seconds (0h:0m:5s) 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, 1.018 / Estimate: 0.000, 0.482 / LogL: -21159.749 Init pinv, alpha: 0.038, 1.018 / Estimate: 0.040, 0.528 / LogL: -21157.099 Init pinv, alpha: 0.076, 1.018 / Estimate: 0.079, 0.582 / LogL: -21154.973 Init pinv, alpha: 0.114, 1.018 / Estimate: 0.114, 0.643 / LogL: -21153.446 Init pinv, alpha: 0.153, 1.018 / Estimate: 0.144, 0.707 / LogL: -21152.668 Init pinv, alpha: 0.191, 1.018 / Estimate: 0.171, 0.775 / LogL: -21152.635 Init pinv, alpha: 0.229, 1.018 / Estimate: 0.184, 0.808 / LogL: -21152.856 Init pinv, alpha: 0.267, 1.018 / Estimate: 0.187, 0.818 / LogL: -21152.924 Init pinv, alpha: 0.305, 1.018 / Estimate: 0.186, 0.814 / LogL: -21152.890 Init pinv, alpha: 0.343, 1.018 / Estimate: 0.188, 0.819 / LogL: -21152.938 Optimal pinv,alpha: 0.171, 0.775 / LogL: -21152.635 Parameters optimization took 2.368 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00171458 secs using 99.5% CPU Computing ML distances took 0.001905 sec (of wall-clock time) 0.001860 sec (of CPU time) Setting up auxiliary I and S matrices: done in 5.3644e-05 secs using 98.8% CPU Computing RapidNJ tree took 0.000251 sec (of wall-clock time) 0.000160 sec (of CPU time) Log-likelihood of RapidNJ tree: -21161.727 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.226 second Computing log-likelihood of 98 initial trees ... 0.469 seconds Current best score: -21152.635 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.604 Iteration 10 / LogL: -21158.103 / Time: 0h:0m:8s Iteration 20 / LogL: -21152.897 / Time: 0h:0m:9s Finish initializing candidate tree set (2) Current best tree score: -21152.604 / CPU time: 1.773 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21157.895 / Time: 0h:0m:10s (0h:0m:11s left) Iteration 40 / LogL: -21152.680 / Time: 0h:0m:10s (0h:0m:8s left) Iteration 50 / LogL: -21157.795 / Time: 0h:0m:11s (0h:0m:6s left) Iteration 60 / LogL: -21152.803 / Time: 0h:0m:12s (0h:0m:4s left) Iteration 70 / LogL: -21152.637 / Time: 0h:0m:12s (0h:0m:3s left) Iteration 80 / LogL: -21152.666 / Time: 0h:0m:13s (0h:0m:2s left) Iteration 90 / LogL: -21157.942 / Time: 0h:0m:13s (0h:0m:1s left) Iteration 100 / LogL: -21152.726 / Time: 0h:0m:14s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:14s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.604 2. Current log-likelihood: -21152.535 Optimal log-likelihood: -21152.526 Rate parameters: A-C: 5.66782 A-G: 7.76633 A-T: 5.66782 C-G: 1.00000 C-T: 22.88730 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.169 Gamma shape alpha: 0.765 Parameters optimization took 2 rounds (0.036 sec) BEST SCORE FOUND : -21152.526 Total tree length: 4.217 Total number of iterations: 102 CPU time used for tree search: 6.740 sec (0h:0m:6s) Wall-clock time used for tree search: 6.825 sec (0h:0m:6s) Total CPU time used: 14.524 sec (0h:0m:14s) Total wall-clock time used: 14.657 sec (0h:0m:14s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Sun Apr 19 08:09:02 2026 14.52user 0.10system 0:14.67elapsed 99%CPU (0avgtext+0avgdata 18056maxresident)k 0inputs+128outputs (0major+4265minor)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 Apr 12 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: 291952 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sun Apr 19 08:09:02 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 17 sequences with 1998 columns, 1152 distinct patterns 1009 parsimony-informative, 303 singleton sites, 686 constant sites Gap/Ambiguity Composition p-value Analyzing sequences: done in 4.4474e-05 secs 1 LngfishAu 0.15% passed 6.20% 2 LngfishSA 0.00% failed 0.62% 3 LngfishAf 0.05% failed 1.60% 4 Frog 0.05% passed 58.01% 5 Turtle 0.15% passed 44.25% 6 Sphenodon 0.10% passed 59.78% 7 Lizard 0.90% passed 38.67% 8 Crocodile 0.35% failed 2.51% 9 Bird 0.00% failed 0.00% 10 Human 0.00% failed 0.85% 11 Seal 0.00% passed 68.93% 12 Cow 0.00% passed 59.11% 13 Whale 0.00% passed 97.83% 14 Mouse 0.05% failed 1.43% 15 Rat 0.00% passed 39.69% 16 Platypus 0.00% failed 3.46% 17 Opossum 0.00% failed 0.01% **** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 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: -21149.239 Optimal log-likelihood: -21149.100 Rate parameters: A-C: 3.73650 A-G: 5.18609 A-T: 3.83480 C-G: 0.41900 C-T: 15.29543 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 Gamma shape alpha: 0.739 Parameters optimization took 1 rounds (0.033 sec) Time for fast ML tree search: 0.350 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 1998 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 22701.500 39 45481.000 45482.593 45699.396 2 GTR+F+I 21615.547 40 43311.094 43312.770 43535.090 3 GTR+F+G4 21155.970 40 42391.940 42393.616 42615.936 4 GTR+F+I+G4 21148.849 41 42379.699 42381.459 42609.295 5 GTR+F+R2 21235.660 41 42553.320 42555.081 42782.916 6 GTR+F+R3 21147.079 43 42380.157 42382.094 42620.953 7 GTR+F+R4 21146.626 45 42383.252 42385.373 42635.247 14 GTR+F+I+R2 21174.433 42 42432.866 42434.714 42668.062 15 GTR+F+I+R3 21146.997 44 42381.994 42384.022 42628.390 16 GTR+F+I+R4 21146.784 46 42385.568 42387.785 42643.164 25 SYM+G4 21317.766 37 42709.531 42710.966 42916.728 26 SYM+I+G4 21306.372 38 42688.744 42690.257 42901.540 47 TVM+F+G4 21300.229 39 42678.458 42680.051 42896.854 48 TVM+F+I+G4 21288.393 40 42656.786 42658.462 42880.782 69 TVMe+G4 21422.115 36 42916.230 42917.589 43117.827 70 TVMe+I+G4 21407.658 37 42889.317 42890.751 43096.513 91 TIM3+F+G4 21367.928 38 42811.857 42813.370 43024.653 92 TIM3+F+I+G4 21359.551 39 42797.102 42798.696 43015.498 113 TIM3e+G4 21717.449 35 43504.899 43506.183 43700.895 114 TIM3e+I+G4 21708.477 36 43488.954 43490.313 43690.551 135 TIM2+F+G4 21159.731 38 42395.462 42396.975 42608.259 136 TIM2+F+I+G4 21152.613 39 42383.226 42384.820 42601.623 157 TIM2e+G4 21320.879 35 42711.758 42713.042 42907.754 158 TIM2e+I+G4 21309.057 36 42690.113 42691.472 42891.710 179 TIM+F+G4 21368.784 38 42813.567 42815.080 43026.364 180 TIM+F+I+G4 21360.272 39 42798.545 42800.138 43016.941 201 TIMe+G4 21718.123 35 43506.246 43507.531 43702.243 202 TIMe+I+G4 21709.148 36 43490.297 43491.655 43691.893 223 TPM3u+F+G4 21488.913 37 43051.825 43053.260 43259.022 224 TPM3u+F+I+G4 21474.794 38 43025.588 43027.101 43238.385 245 TPM3+G4 21847.238 34 43762.476 43763.689 43952.873 246 TPM3+I+G4 21833.461 35 43736.923 43738.207 43932.919 267 TPM2u+F+G4 21303.761 37 42681.522 42682.956 42888.718 268 TPM2u+F+I+G4 21291.570 38 42659.139 42660.652 42871.936 289 TPM2+G4 21424.804 34 42917.607 42918.820 43108.004 290 TPM2+I+G4 21410.107 35 42890.214 42891.498 43086.210 311 K3Pu+F+G4 21489.344 37 43052.688 43054.122 43259.884 312 K3Pu+F+I+G4 21475.259 38 43026.519 43028.032 43239.315 333 K3P+G4 21847.491 34 43762.981 43764.194 43953.378 334 K3P+I+G4 21833.614 35 43737.229 43738.513 43933.225 355 TN+F+G4 21369.057 37 42812.114 42813.549 43019.310 356 TN+F+I+G4 21360.716 38 42797.432 42798.945 43010.228 377 TNe+G4 21718.193 34 43504.387 43505.599 43694.783 378 TNe+I+G4 21709.196 35 43488.392 43489.677 43684.389 399 HKY+F+G4 21489.748 36 43051.496 43052.854 43253.092 400 HKY+F+I+G4 21475.591 37 43025.182 43026.617 43232.378 421 K2P+G4 21847.674 33 43761.348 43762.491 43946.145 422 K2P+I+G4 21833.840 34 43735.679 43736.892 43926.076 443 F81+F+G4 22031.579 35 44133.158 44134.443 44329.155 444 F81+F+I+G4 22019.146 36 44110.291 44111.650 44311.888 465 JC+G4 22258.086 32 44580.171 44581.246 44759.368 466 JC+I+G4 22245.386 33 44556.771 44557.914 44741.568 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 5.623 seconds (0h:0m:5s) Wall-clock time for ModelFinder: 5.685 seconds (0h:0m:5s) 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, 1.018 / Estimate: 0.000, 0.482 / LogL: -21159.749 Init pinv, alpha: 0.038, 1.018 / Estimate: 0.040, 0.528 / LogL: -21157.099 Init pinv, alpha: 0.076, 1.018 / Estimate: 0.079, 0.582 / LogL: -21154.973 Init pinv, alpha: 0.114, 1.018 / Estimate: 0.114, 0.643 / LogL: -21153.446 Init pinv, alpha: 0.153, 1.018 / Estimate: 0.144, 0.707 / LogL: -21152.668 Init pinv, alpha: 0.191, 1.018 / Estimate: 0.171, 0.775 / LogL: -21152.635 Init pinv, alpha: 0.229, 1.018 / Estimate: 0.184, 0.808 / LogL: -21152.856 Init pinv, alpha: 0.267, 1.018 / Estimate: 0.187, 0.818 / LogL: -21152.924 Init pinv, alpha: 0.305, 1.018 / Estimate: 0.186, 0.814 / LogL: -21152.890 Init pinv, alpha: 0.343, 1.018 / Estimate: 0.188, 0.819 / LogL: -21152.938 Optimal pinv,alpha: 0.171, 0.775 / LogL: -21152.635 Parameters optimization took 2.166 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.0016169 secs using 95% CPU Computing ML distances took 0.001849 sec (of wall-clock time) 0.001708 sec (of CPU time) Setting up auxiliary I and S matrices: done in 3.7342e-05 secs using 99.08% CPU Computing RapidNJ tree took 0.000171 sec (of wall-clock time) 0.000349 sec (of CPU time) Log-likelihood of RapidNJ tree: -21161.727 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.203 second Computing log-likelihood of 98 initial trees ... 0.423 seconds Current best score: -21152.635 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.604 Iteration 10 / LogL: -21152.839 / Time: 0h:0m:8s Iteration 20 / LogL: -21158.046 / Time: 0h:0m:9s Finish initializing candidate tree set (2) Current best tree score: -21152.604 / CPU time: 1.538 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.613 / Time: 0h:0m:9s (0h:0m:10s left) Iteration 40 / LogL: -21154.952 / Time: 0h:0m:10s (0h:0m:7s left) Iteration 50 / LogL: -21157.959 / Time: 0h:0m:11s (0h:0m:5s left) Iteration 60 / LogL: -21152.801 / Time: 0h:0m:11s (0h:0m:4s left) Iteration 70 / LogL: -21153.302 / Time: 0h:0m:12s (0h:0m:2s left) Iteration 80 / LogL: -21152.749 / Time: 0h:0m:12s (0h:0m:1s left) Iteration 90 / LogL: -21152.623 / Time: 0h:0m:13s (0h:0m:0s left) Iteration 100 / LogL: -21152.739 / Time: 0h:0m:13s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:14s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.604 2. Current log-likelihood: -21152.535 Optimal log-likelihood: -21152.526 Rate parameters: A-C: 5.66782 A-G: 7.76633 A-T: 5.66782 C-G: 1.00000 C-T: 22.88730 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.169 Gamma shape alpha: 0.765 Parameters optimization took 2 rounds (0.036 sec) BEST SCORE FOUND : -21152.526 Total tree length: 4.217 Total number of iterations: 102 CPU time used for tree search: 6.105 sec (0h:0m:6s) Wall-clock time used for tree search: 6.161 sec (0h:0m:6s) Total CPU time used: 13.948 sec (0h:0m:13s) Total wall-clock time used: 14.076 sec (0h:0m:14s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Sun Apr 19 08:09:16 2026 13.94user 0.11system 0:14.09elapsed 99%CPU (0avgtext+0avgdata 18596maxresident)k 0inputs+128outputs (0major+7070minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.9eRf7j 28.50user 0.23system 0:28.80elapsed 99%CPU (0avgtext+0avgdata 18596maxresident)k 0inputs+336outputs (0major+13046minor)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-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree_2.4.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree_2.4.0+dfsg-1_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 2026-04-19T08:10:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 19 Apr 2026 08:10:59 +0000 | +------------------------------------------------------------------------------+ iqtree_2.4.0+dfsg-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Sun, 12 Apr 2026 11:18:58 +0200 Source: iqtree Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.4.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: iqtree - efficient phylogenetic software by maximum likelihood Changes: iqtree (2.4.0+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream location for legacy IQ-TREE version 2.x. Updated primary citation as well. * New upstream version * Standards-Version: 4.7.4 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * debputy lint --auto-fix (routine-update) * d/patches: refreshed, dropped 2 no-longer needed: boost1.90 & gcc- 15. * d/watch: download using git, due to submodules. * Added patch to use googletest & yaml-cpp packages. * d/rules: add openmpi include path * Disable building on i386, as per upstream. Checksums-Sha1: b5a7ed5b632388bcc4a6cc4c72ffbd4e30f9672b 115232852 iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb bb4be06df17947739a477f657a4fc82c07a048be 8755 iqtree_2.4.0+dfsg-1_amd64.buildinfo 8eda53a6ec376df87f8b0916838f24db68fbf0de 10315820 iqtree_2.4.0+dfsg-1_amd64.deb Checksums-Sha256: 20008f64d12e274e9e4cd3307927f0909ed1d660ba2e6793a2b4445da6cdc065 115232852 iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb cc3205240678775359d99bb3ec0d2e09aa94decc079f976060319d5e43ca27f5 8755 iqtree_2.4.0+dfsg-1_amd64.buildinfo bed0572481dbd808208f5da0d1e145d6c5fdd32ab9f3637a8280de28d4f6513f 10315820 iqtree_2.4.0+dfsg-1_amd64.deb Files: fab4f00bdef6c85f921300b072ac8456 115232852 debug optional iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb 822865080bb52e9a1c26299e4fdc7bd5 8755 science optional iqtree_2.4.0+dfsg-1_amd64.buildinfo 69c2e04cae332ef0081c62d0a4fffdd8 10315820 science optional iqtree_2.4.0+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 19 Apr 2026 08:10:59 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree Binary: iqtree iqtree-dbgsym Architecture: amd64 Version: 2.4.0+dfsg-1 Checksums-Md5: fab4f00bdef6c85f921300b072ac8456 115232852 iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb 69c2e04cae332ef0081c62d0a4fffdd8 10315820 iqtree_2.4.0+dfsg-1_amd64.deb Checksums-Sha1: b5a7ed5b632388bcc4a6cc4c72ffbd4e30f9672b 115232852 iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb 8eda53a6ec376df87f8b0916838f24db68fbf0de 10315820 iqtree_2.4.0+dfsg-1_amd64.deb Checksums-Sha256: 20008f64d12e274e9e4cd3307927f0909ed1d660ba2e6793a2b4445da6cdc065 115232852 iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb bed0572481dbd808208f5da0d1e145d6c5fdd32ab9f3637a8280de28d4f6513f 10315820 iqtree_2.4.0+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 19 Apr 2026 08:10:57 +0000 Build-Path: /build/reproducible-path/iqtree-2.4.0+dfsg Installed-Build-Depends: adduser (= 3.155), autoconf (= 2.72-6), automake (= 1:1.18.1-4), autopoint (= 0.23.2-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.42-3), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), chrpath (= 0.18-1), cmake (= 4.3.1-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-16), cpp-15-x86-64-linux-gnu (= 15.2.0-16), cpp-x86-64-linux-gnu (= 4:15.2.0-5), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-16), g++-15-x86-64-linux-gnu (= 15.2.0-16), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-16), gcc-15-base (= 15.2.0-16), gcc-15-x86-64-linux-gnu (= 15.2.0-16), gcc-16-base (= 16-20260322-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-2), gettext-base (= 0.23.2-2), gfortran-15 (= 15.2.0-16), gfortran-15-x86-64-linux-gnu (= 15.2.0-16), googletest (= 1.17.0-1), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 61.0-2), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.5-1), libasan8 (= 16-20260322-1), libatomic1 (= 16-20260322-1), 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 (= 2.42-3), libboost-dev (= 1.90.0.1), libboost1.90-dev (= 1.90.0-6), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-2+b1), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-14), libc-dev-bin (= 2.42-14), libc-gconv-modules-extra (= 2.42-14), libc6 (= 2.42-14), libc6-dev (= 2.42-14), libcap-ng0 (= 0.9.2-1), libcbor0.10 (= 0.10.2-2.1), libcc1-0 (= 16-20260322-1), libclang-common-21-dev (= 1:21.1.8-7), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl4t64 (= 8.19.0-3), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.31), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.131-1), libdrm-common (= 2.4.131-1), libdrm2 (= 2.4.131-1), libedit2 (= 3.1-20251016-1), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.194-4), 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 (= 2.7.5-1), libfabric1 (= 2.1.0-1.1+b1), libffi8 (= 3.5.2-4), libfido2-1 (= 1.16.0-2+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libfuse3-4 (= 3.18.2-1), libgcc-15-dev (= 15.2.0-16), libgcc-s1 (= 16-20260322-1), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgfortran-15-dev (= 15.2.0-16), libgfortran5 (= 16-20260322-1), libgmp-dev (= 2:6.3.0+dfsg-5+b1), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b1), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 16-20260322-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2+b1), libhogweed6t64 (= 3.10.2-1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16-20260322-1), libhwloc-dev (= 2.13.0-2), libhwloc-plugins (= 2.13.0-2), libhwloc15 (= 2.13.0-2), libibmad5 (= 61.0-2), libibumad3 (= 61.0-2), libibverbs-dev (= 61.0-2), libibverbs1 (= 61.0-2), libidn2-0 (= 2.3.8-4+b1), libisl23 (= 0.27-2), libitm1 (= 16-20260322-1), libjansson4 (= 2.14-2+b4), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp26 (= 1.9.6-5+b1), libk5crypto3 (= 1.22.1-2+b1), libkeyutils1 (= 1.6.3-6+b1), libkrb5-3 (= 1.22.1-2+b1), libkrb5support0 (= 1.22.1-2+b1), libldap2 (= 2.6.10+dfsg-1+b1), libllvm21 (= 1:21.1.8-7), liblocale-gettext-perl (= 1.07-8), liblsan0 (= 16-20260322-1), libltdl-dev (= 2.5.4-10), libltdl7 (= 2.5.4-10), liblz4-1 (= 1.10.0-8), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.42-3), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncursesw6 (= 6.6+20251231-1), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.68.1-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.21.0-1), libngtcp2-crypto-ossl0 (= 1.21.0-1), libnl-3-200 (= 3.12.0-2), libnl-3-dev (= 3.12.0-2), libnl-route-3-200 (= 3.12.0-2), libnl-route-3-dev (= 3.12.0-2), libnuma-dev (= 2.0.19-1+b1), libnuma1 (= 2.0.19-1+b1), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libp11-kit0 (= 0.26.2-2), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2+b1), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 6.0.0+really5.0.9-3), libproc2-0 (= 2:4.0.4-9+b1), 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 (= 16-20260322-1), librdmacm1t64 (= 61.0-2), librhash1 (= 1.4.6-1.1), librtmp1 (= 2.6-1), 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), libsemanage-common (= 3.10-1), libsemanage2 (= 3.10-1), libsepol2 (= 3.10-1), libsframe3 (= 2.46-3), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42-3), libsprng2 (= 2.0a-19), libsprng2-dev (= 2.0a-19), libssh2-1t64 (= 1.11.1-2), libssl3t64 (= 3.6.1-3), libstdc++-15-dev (= 15.2.0-16), libstdc++6 (= 16-20260322-1), libsystemd-shared (= 260.1-1), libsystemd0 (= 260.1-1), libtasn1-6 (= 4.21.0-2), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-10), libtsan2 (= 16-20260322-1), libubsan1 (= 16-20260322-1), libucc1 (= 1.7.0~rc1-1), libuchardet0 (= 0.0.8-2+b1), libucx0 (= 1.20.1~rc1-2), libudev1 (= 260.1-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42-3), libuv1t64 (= 1.51.0-2+b1), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b1), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.2+dfsg-0.1), libxnvctrl0 (= 535.171.04-1+b3), libxxhash0 (= 0.8.3-2+b1), libyaml-cpp-dev (= 0.8.0+dfsg-9), libyaml-cpp0.8 (= 0.8.0+dfsg-9), libz3-4 (= 4.13.3-1+b1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.19.11-1), login.defs (= 1:4.19.3-2), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.42-3), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), ocl-icd-libopencl1 (= 2.3.4-1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.2p1-6), openssl-provider-legacy (= 3.6.1-3), passwd (= 1:4.19.3-2), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), 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+b1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), systemd (= 260.1-1), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.9-0.4), util-linux (= 2.42-3), 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="1775985538" +------------------------------------------------------------------------------+ | Package contents Sun, 19 Apr 2026 08:11:00 +0000 | +------------------------------------------------------------------------------+ iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 115232852 bytes: control archive=700 bytes. 461 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: iqtree-dbgsym Source: iqtree Version: 2.4.0+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 122112 Depends: iqtree (= 2.4.0+dfsg-1) Section: debug Priority: optional Description: debug symbols for iqtree Build-Ids: 38c8aa77dff3ba8554ec787e6c9559b2db9ec8f4 a762e5f914bbeee04c14ea760f669c1af90821d0 a9b17513bcc3eb10837e348bbddeae9be39678ee drwxr-xr-x root/root 0 2026-04-12 09:18 ./ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.build-id/38/ -rw-r--r-- root/root 36224520 2026-04-12 09:18 ./usr/lib/debug/.build-id/38/c8aa77dff3ba8554ec787e6c9559b2db9ec8f4.debug drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.build-id/a7/ -rw-r--r-- root/root 36316912 2026-04-12 09:18 ./usr/lib/debug/.build-id/a7/62e5f914bbeee04c14ea760f669c1af90821d0.debug drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.build-id/a9/ -rw-r--r-- root/root 36224280 2026-04-12 09:18 ./usr/lib/debug/.build-id/a9/b17513bcc3eb10837e348bbddeae9be39678ee.debug drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 16260112 2026-04-12 09:18 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree.debug drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-12 09:18 ./usr/share/doc/iqtree-dbgsym -> iqtree iqtree_2.4.0+dfsg-1_amd64.deb ----------------------------- new Debian package, version 2.0. size 10315820 bytes: control archive=1544 bytes. 1436 bytes, 29 lines control 1104 bytes, 16 lines md5sums Package: iqtree Version: 2.4.0+dfsg-1 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 2026-04-12 09:18 ./ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/bin/ -rwxr-xr-x root/root 11020920 2026-04-12 09:18 ./usr/bin/iqtree2 -rwxr-xr-x root/root 11037304 2026-04-12 09:18 ./usr/bin/iqtree2-mpi -rwxr-xr-x root/root 11020920 2026-04-12 09:18 ./usr/bin/iqtree2-omp drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/doc/iqtree/ -rw-r--r-- root/root 278 2026-04-10 16:10 ./usr/share/doc/iqtree/README.test -rw-r--r-- root/root 990 2026-04-12 09:18 ./usr/share/doc/iqtree/changelog.Debian.gz -rw-r--r-- root/root 8147 2026-04-11 13:32 ./usr/share/doc/iqtree/copyright drwxr-xr-x root/root 0 2026-04-12 09:18 ./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 2026-04-10 16:10 ./usr/share/doc/iqtree/run-unit-test drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/man/ drwxr-xr-x root/root 0 2026-04-12 09:18 ./usr/share/man/man1/ -rw-r--r-- root/root 6971 2026-04-12 09:18 ./usr/share/man/man1/iqtree2-mpi.1.gz -rw-r--r-- root/root 6969 2026-04-12 09:18 ./usr/share/man/man1/iqtree2-omp.1.gz -rw-r--r-- root/root 6951 2026-04-12 09:18 ./usr/share/man/man1/iqtree2.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 19 Apr 2026 08:11:01 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 19 Apr 2026 08:11:01 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 19 Apr 2026 08:11:03 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3337976 Build-Time: 818 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdDDMXKo/inputs/iqtree_2.4.0+dfsg-1.dsc Machine Architecture: amd64 Package: iqtree Package-Time: 829 Source-Version: 2.4.0+dfsg-1 Space: 3337976 Status: successful Version: 2.4.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 2026-04-19T08:10:58Z Build needed 00:13:49, 3337976k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdDDMXKo/out checking iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb: size differs for iqtree-dbgsym_2.4.0+dfsg-1_amd64.deb